[{"external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"date_published":"2020-09-23T00:00:00Z","date_created":"2020-08-14T09:36:05Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","intvolume":" 107","year":"2020","oa":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","description":"News on IST Website","relation":"press_release"}]},"page":"1212-1225","article_type":"original","publication":"Neuron","date_updated":"2023-08-22T08:30:55Z","oa_version":"Published Version","citation":{"apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006."},"day":"23","ddc":["570"],"file_date_updated":"2020-12-04T09:29:21Z","month":"09","pmid":1,"has_accepted_license":"1","volume":107,"article_processing_charge":"No","file":[{"file_id":"8920","date_created":"2020-12-04T09:29:21Z","file_name":"2020_Neuron_Zhang.pdf","creator":"dernst","relation":"main_file","file_size":3011120,"access_level":"open_access","checksum":"44a5960fc083a4cb3488d22224859fdc","content_type":"application/pdf","success":1,"date_updated":"2020-12-04T09:29:21Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion."}],"issue":"6","doi":"10.1016/j.neuron.2020.07.006","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","author":[{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","full_name":"Zhang, Xiaomin","last_name":"Zhang"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"_id":"8261","publication_status":"published","status":"public","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","ec_funded":1,"publication_identifier":{"issn":["0896-6273"]},"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}]},{"publisher":"IEEE","intvolume":" 68","main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"date_published":"2020-07-20T00:00:00Z","date_created":"2020-08-16T22:00:56Z","scopus_import":"1","publication":"IEEE Transactions on Signal Processing","date_updated":"2023-08-22T08:40:08Z","page":"4268-4282","article_type":"original","oa":1,"year":"2020","arxiv":1,"volume":68,"article_processing_charge":"No","citation":{"mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355","ieee":"N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020."},"day":"20","month":"07","oa_version":"Preprint","publication_identifier":{"issn":["1053587X"],"eissn":["19410476"]},"acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","publication_status":"published","status":"public","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","author":[{"last_name":"Gurel","full_name":"Gurel, Nezihe Merve","first_name":"Nezihe Merve"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"full_name":"Stojanov, Alen","last_name":"Stojanov","first_name":"Alen"},{"last_name":"Smith","full_name":"Smith, Tyler","first_name":"Tyler"},{"first_name":"Thomas","full_name":"Lemmin, Thomas","last_name":"Lemmin"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"first_name":"Markus","last_name":"Puschel","full_name":"Puschel, Markus"},{"last_name":"Zhang","full_name":"Zhang, Ce","first_name":"Ce"}],"_id":"8268","abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"doi":"10.1109/TSP.2020.3010355"},{"publication":"Molecular Plant","date_updated":"2023-08-22T08:40:35Z","article_type":"original","page":"1238-1240","year":"2020","intvolume":" 13","publisher":"Elsevier","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000566895400007"],"pmid":["32688032"]},"date_published":"2020-09-07T00:00:00Z","scopus_import":"1","date_created":"2020-08-16T22:00:57Z","publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","publication_status":"published","status":"public","author":[{"first_name":"Peng","full_name":"He, Peng","last_name":"He"},{"last_name":"Zhang","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956"},{"first_name":"Guanghui","full_name":"Xiao, Guanghui","last_name":"Xiao"}],"title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","_id":"8271","issue":"9","doi":"10.1016/j.molp.2020.07.006","volume":13,"article_processing_charge":"No","day":"07","citation":{"mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006.","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","apa":"He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006","ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240."},"pmid":1,"month":"09","oa_version":"None"},{"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Katoen, Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"},{"last_name":"Winkler","full_name":"Winkler, Tobias","first_name":"Tobias"}],"title":"Stochastic games with lexicographic reachability-safety objectives","_id":"8272","abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"doi":"10.1007/978-3-030-53291-8_21","publication_identifier":{"eissn":["16113349"],"issn":["03029743"],"isbn":["9783030532901"]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"publication_status":"published","status":"public","ec_funded":1,"day":"14","citation":{"mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420."},"ddc":["000"],"month":"07","file_date_updated":"2020-08-17T11:32:44Z","conference":{"name":"CAV: Computer Aided Verification"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"date_created":"2020-08-17T11:32:44Z","file_id":"8276","relation":"main_file","file_size":625056,"creator":"dernst","file_name":"2020_LNCS_CAV_Chatterjee.pdf","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-08-17T11:32:44Z","success":1}],"has_accepted_license":"1","volume":12225,"article_processing_charge":"No","oa":1,"alternative_title":["LNCS"],"year":"2020","publication":"International Conference on Computer Aided Verification","date_updated":"2025-07-14T09:10:14Z","related_material":{"record":[{"id":"12738","status":"public","relation":"later_version"}]},"page":"398-420","department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"date_published":"2020-07-14T00:00:00Z","scopus_import":"1","date_created":"2020-08-16T22:00:58Z","intvolume":" 12225","publisher":"Springer Nature","isi":1,"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}]},{"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"article_type":"original","article_number":"5272","publication":"International Journal of Molecular Sciences","date_updated":"2024-10-29T10:22:43Z","year":"2020","oa":1,"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 21","publisher":"MDPI","external_id":{"isi":["000565090300001"],"pmid":["32785037"]},"date_published":"2020-08-10T00:00:00Z","scopus_import":"1","date_created":"2020-08-24T06:24:03Z","department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","status":"public","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"issue":"16","abstract":[{"text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. ","lang":"eng"}],"doi":"10.3390/ijms21165727","author":[{"first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang"},{"first_name":"Linyi","last_name":"Lai","full_name":"Lai, Linyi"},{"orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Liu, Liping","last_name":"Liu","first_name":"Liping"},{"first_name":"Bello Hassan","full_name":"Jakada, Bello Hassan","last_name":"Jakada"},{"first_name":"Youmei","last_name":"Huang","full_name":"Huang, Youmei"},{"first_name":"Qing","full_name":"He, Qing","last_name":"He"},{"first_name":"Mengnan","last_name":"Chai","full_name":"Chai, Mengnan"},{"full_name":"Niu, Xiaoping","last_name":"Niu","first_name":"Xiaoping"},{"first_name":"Yuan","full_name":"Qin, Yuan","last_name":"Qin"}],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","_id":"8283","has_accepted_license":"1","volume":21,"article_processing_charge":"No","file":[{"date_created":"2020-08-25T09:53:50Z","file_id":"8292","date_updated":"2020-08-25T09:53:50Z","success":1,"checksum":"03b039244e6ae80580385fd9f577e2b2","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cziletti","file_size":5718755,"file_name":"2020_IntMolecSciences_Chen.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"10","citation":{"mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020)."},"pmid":1,"file_date_updated":"2020-08-25T09:53:50Z","month":"08","ddc":["570"]},{"intvolume":" 9","publisher":"eLife Sciences Publications","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"date_published":"2020-07-31T00:00:00Z","scopus_import":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_created":"2020-08-24T06:24:04Z","publication":"eLife","date_updated":"2023-09-07T13:14:08Z","related_material":{"record":[{"id":"8353","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage","relation":"press_release"}]},"article_type":"original","article_number":"e59407","oa":1,"year":"2020","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-08-24T13:31:53Z","success":1,"content_type":"application/pdf","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","access_level":"open_access","file_size":7320493,"relation":"main_file","creator":"cziletti","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","file_id":"8289"}],"has_accepted_license":"1","article_processing_charge":"No","volume":9,"day":"31","citation":{"short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407."},"month":"07","pmid":1,"ddc":["570"],"file_date_updated":"2020-08-24T13:31:53Z","oa_version":"Published Version","publication_identifier":{"eissn":["2050084X"]},"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","status":"public","publication_status":"published","author":[{"last_name":"Steiner","full_name":"Steiner, Julia","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","_id":"8284","abstract":[{"lang":"eng","text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements."}],"doi":"10.7554/eLife.59407"},{"article_type":"original","article_number":"043202","publication":"Physical Review Letters","date_updated":"2023-10-18T08:38:35Z","year":"2020","oa":1,"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"intvolume":" 125","publisher":"American Physical Society","date_published":"2020-07-24T00:00:00Z","external_id":{"pmid":["32794788"],"arxiv":["1912.10218"],"isi":["000552227400008"]},"scopus_import":"1","date_created":"2020-08-24T06:24:04Z","department":[{"_id":"OnHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","publication_status":"published","status":"public","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"issue":"4","abstract":[{"text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.","lang":"eng"}],"doi":"10.1103/PhysRevLett.125.043202","author":[{"last_name":"Malia","full_name":"Malia, Benjamin K.","first_name":"Benjamin K."},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"first_name":"Yunfan","last_name":"Wu","full_name":"Wu, Yunfan"},{"last_name":"Hosten","full_name":"Hosten, Onur","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","_id":"8285","volume":125,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","day":"24","citation":{"ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202."},"month":"07","pmid":1},{"date_updated":"2023-08-22T13:27:32Z","publication":"Proceedings of the International Conference on Embedded Software","related_material":{"record":[{"relation":"later_version","status":"public","id":"8790"}]},"oa":1,"keyword":["reachability","hybrid systems","decomposition"],"year":"2020","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"ToHe"}],"date_created":"2020-08-24T12:56:20Z","date_published":"2020-01-01T00:00:00Z","external_id":{"arxiv":["1905.02458"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"ec_funded":1,"publication_status":"published","status":"public","_id":"8287","author":[{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","first_name":"Sergiy"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","last_name":"Potomkin","first_name":"Kostiantyn"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065"}],"title":"Reachability analysis of linear hybrid systems via block decomposition","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"file":[{"relation":"main_file","file_size":696384,"creator":"cschilli","file_name":"2020EMSOFT.pdf","date_updated":"2020-08-24T12:53:15Z","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75","content_type":"application/pdf","access_level":"open_access","date_created":"2020-08-24T12:53:15Z","file_id":"8288"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"article_processing_charge":"No","has_accepted_license":"1","ddc":["000"],"file_date_updated":"2020-08-24T12:53:15Z","citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020."},"conference":{"name":"EMSOFT: International Conference on Embedded Software","start_date":"2020-09-20","location":"Virtual ","end_date":"2020-09-25"},"oa_version":"Preprint"},{"year":"2020","oa":1,"article_type":"original","article_number":"060202(R)","related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-08-24T14:20:21Z","publication":"Physical Review B","scopus_import":"1","date_created":"2020-08-26T19:27:42Z","external_id":{"isi":["000562628300001"]},"date_published":"2020-08-26T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":" 102","publisher":"American Physical Society","doi":"10.1103/physrevb.102.060202","issue":"6","abstract":[{"lang":"eng","text":"Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model."}],"_id":"8308","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"title":"Stability of mobility edges in disordered interacting systems","ec_funded":1,"acknowledgement":"Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).","publication_status":"published","status":"public","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"oa_version":"None","file_date_updated":"2020-08-26T19:29:00Z","ddc":["530"],"month":"08","day":"26","citation":{"ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. Physical Review B. 2020;102(6). doi:10.1103/physrevb.102.060202","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” Physical Review B, vol. 102, no. 6. American Physical Society, 2020.","apa":"Brighi, P., Abanin, D. A., & Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.060202","mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:10.1103/physrevb.102.060202.","chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.060202."},"article_processing_charge":"No","volume":102,"has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"716442fa7861323fcc80b93718ca009c","content_type":"application/pdf","success":1,"date_updated":"2020-08-26T19:28:55Z","file_name":"PhysRevB.102.060202.pdf","file_size":488825,"relation":"main_file","creator":"mserbyn","file_id":"8309","date_created":"2020-08-26T19:28:55Z"},{"access_level":"open_access","content_type":"application/pdf","checksum":"be0abdc8f60fe065ea6dc92e08487122","success":1,"date_updated":"2020-08-26T19:29:00Z","file_name":"Supplementary-mbme.pdf","creator":"mserbyn","relation":"main_file","file_size":711405,"file_id":"8310","date_created":"2020-08-26T19:29:00Z"}]},{"intvolume":" 11","publisher":"Springer Nature","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LeSa"}],"scopus_import":"1","date_created":"2020-08-30T22:01:10Z","external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"date_published":"2020-08-18T00:00:00Z","date_updated":"2023-08-22T09:03:00Z","publication":"Nature Communications","article_type":"original","article_number":"4135","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release"}]},"oa":1,"year":"2020","file":[{"file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","creator":"cziletti","relation":"main_file","file_size":7527373,"success":1,"date_updated":"2020-08-31T13:40:00Z","access_level":"open_access","content_type":"application/pdf","checksum":"52b96f41d7d0db9728064c08da00d030","file_id":"8326","date_created":"2020-08-31T13:40:00Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"file_date_updated":"2020-08-31T13:40:00Z","month":"08","pmid":1,"day":"18","citation":{"chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0.","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135."},"oa_version":"Published Version","publication_identifier":{"eissn":["20411723"]},"acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","publication_status":"published","status":"public","_id":"8318","author":[{"full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol"},{"last_name":"Minhas","full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S."},{"last_name":"Baradaran","full_name":"Baradaran, Rozbeh","first_name":"Rozbeh"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","first_name":"Margherita","full_name":"Tambalo, Margherita","last_name":"Tambalo"},{"first_name":"David T.","full_name":"Gallagher, David T.","last_name":"Gallagher"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"title":"Key role of quinone in the mechanism of respiratory complex I","doi":"10.1038/s41467-020-17957-0","issue":"1","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}]},{"oa":1,"year":"2020","date_updated":"2024-02-28T13:11:28Z","publication":"Physical Review A","article_number":"012224","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"OnHo"}],"date_created":"2020-08-30T22:01:10Z","scopus_import":"1","external_id":{"arxiv":["1912.08334"],"isi":["000555104200011"]},"date_published":"2020-07-30T00:00:00Z","publisher":"American Physical Society","intvolume":" 102","main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"_id":"8319","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","author":[{"full_name":"Wu, Yunfan","last_name":"Wu","first_name":"Yunfan"},{"last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv","first_name":"Rajiv"},{"full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón","first_name":"Julián"},{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"orcid":"0000-0002-2031-204X","last_name":"Hosten","full_name":"Hosten, Onur","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark A.","last_name":"Kasevich","full_name":"Kasevich, Mark A."}],"doi":"10.1103/PhysRevA.102.012224","abstract":[{"text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"issue":"1","publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"status":"public","publication_status":"published","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","month":"07","citation":{"ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224."},"day":"30","oa_version":"Preprint","arxiv":1,"volume":102,"article_processing_charge":"No"},{"date_published":"2020-08-19T00:00:00Z","external_id":{"isi":["000562110300001"]},"date_created":"2020-08-30T22:01:11Z","scopus_import":"1","department":[{"_id":"FyKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Springer Nature","intvolume":" 54","year":"2020","related_material":{"record":[{"id":"8321","status":"public","relation":"original"}]},"page":"475-484","article_type":"original","publication":"Molecular Biology","date_updated":"2023-08-22T09:01:03Z","oa_version":"None","citation":{"mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111"},"day":"19","month":"08","article_processing_charge":"No","volume":54,"abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"issue":"4","doi":"10.1134/S0026893320040111","title":"Expanding the genetic code: Unnatural base pairs in biological systems","author":[{"first_name":"S. A.","full_name":"Mukba, S. A.","last_name":"Mukba"},{"full_name":"Vlasov, Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"last_name":"Kolosov","full_name":"Kolosov, P. M.","first_name":"P. M."},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"_id":"8320","status":"public","publication_status":"published","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]}},{"volume":54,"article_processing_charge":"No","oa_version":"None","pmid":1,"month":"07","day":"01","citation":{"mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126"},"publication_status":"published","status":"public","publication_identifier":{"issn":["00268984"]},"doi":"10.31857/S0026898420040126","issue":"4","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"_id":"8321","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"last_name":"Vlasov","full_name":"Vlasov, Petr","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolosov","full_name":"Kolosov, P. M.","first_name":"P. M."},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"first_name":"E. Z.","full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva"}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","language":[{"iso":"rus"}],"quality_controlled":"1","type":"journal_article","intvolume":" 54","publisher":"Russian Academy of Sciences","scopus_import":"1","date_created":"2020-08-30T22:01:11Z","external_id":{"pmid":["32799218"]},"date_published":"2020-07-01T00:00:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"FyKo"}],"article_type":"original","page":"531-541","related_material":{"record":[{"id":"8320","status":"public","relation":"translation"}]},"date_updated":"2023-08-22T09:01:02Z","publication":"Molekuliarnaia biologiia","year":"2020"},{"alternative_title":["LNCS"],"year":"2020","oa":1,"page":"732-762","publication":"Advances in Cryptology – CRYPTO 2020","date_updated":"2021-01-12T08:18:08Z","date_published":"2020-08-10T00:00:00Z","scopus_import":"1","date_created":"2020-08-30T22:01:12Z","department":[{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1317"}],"intvolume":" 12171","publisher":"Springer Nature","abstract":[{"text":"Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.\r\nIn this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.\r\nOur core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).","lang":"eng"}],"doi":"10.1007/978-3-030-56880-1_26","author":[{"first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","full_name":"Chakraborty, Suvradip"},{"last_name":"Dziembowski","full_name":"Dziembowski, Stefan","first_name":"Stefan"},{"first_name":"Jesper Buus","last_name":"Nielsen","full_name":"Nielsen, Jesper Buus"}],"title":"Reverse firewalls for actively secure MPCs","_id":"8322","acknowledgement":"We would like to thank the anonymous reviewers for their helpful comments and suggestions. The work was initiated while the first author was in IIT Madras, India. Part of this work was done while the author was visiting the University of Warsaw. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT) and from the Foundation for Polish Science under grant TEAM/2016-1/4 founded within the UE 2014–2020 Smart Growth Operational Program. The last author was supported by the Independent Research Fund Denmark project BETHE and the Concordium Blockchain Research Center, Aarhus University, Denmark.","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"isbn":["9783030568795"],"issn":["03029743"],"eissn":["16113349"]},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"conference":{"name":"CRYPTO: Annual International Cryptology Conference","end_date":"2020-08-21","location":"Santa Barbara, CA, United States","start_date":"2020-08-17"},"oa_version":"Preprint","day":"10","citation":{"mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Actively Secure MPCs.” Advances in Cryptology – CRYPTO 2020, vol. 12171, Springer Nature, 2020, pp. 732–62, doi:10.1007/978-3-030-56880-1_26.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, and Jesper Buus Nielsen. “Reverse Firewalls for Actively Secure MPCs.” In Advances in Cryptology – CRYPTO 2020, 12171:732–62. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-56880-1_26.","ista":"Chakraborty S, Dziembowski S, Nielsen JB. 2020. Reverse firewalls for actively secure MPCs. Advances in Cryptology – CRYPTO 2020. CRYPTO: Annual International Cryptology Conference, LNCS, vol. 12171, 732–762.","short":"S. Chakraborty, S. Dziembowski, J.B. Nielsen, in:, Advances in Cryptology – CRYPTO 2020, Springer Nature, 2020, pp. 732–762.","ama":"Chakraborty S, Dziembowski S, Nielsen JB. Reverse firewalls for actively secure MPCs. In: Advances in Cryptology – CRYPTO 2020. Vol 12171. Springer Nature; 2020:732-762. doi:10.1007/978-3-030-56880-1_26","ieee":"S. Chakraborty, S. Dziembowski, and J. B. Nielsen, “Reverse firewalls for actively secure MPCs,” in Advances in Cryptology – CRYPTO 2020, Santa Barbara, CA, United States, 2020, vol. 12171, pp. 732–762.","apa":"Chakraborty, S., Dziembowski, S., & Nielsen, J. B. (2020). Reverse firewalls for actively secure MPCs. In Advances in Cryptology – CRYPTO 2020 (Vol. 12171, pp. 732–762). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-56880-1_26"},"month":"08","volume":12171,"article_processing_charge":"No"},{"year":"2020","oa":1,"page":"571-574","article_type":"letter_note","date_updated":"2023-08-22T09:05:04Z","publication":"Discrete and Computational Geometry","date_created":"2020-08-30T22:01:12Z","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","external_id":{"isi":["000561483500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":" 64","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"doi":"10.1007/s00454-020-00237-5","_id":"8323","title":"A farewell to Ricky Pollack","author":[{"last_name":"Pach","full_name":"Pach, János","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"status":"public","publication_status":"published","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"oa_version":"None","month":"10","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574."},"day":"01","article_processing_charge":"No","volume":64},{"publication":"Proceedings of the ACM on Programming Languages","date_updated":"2024-02-22T15:16:45Z","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.3533633","relation":"software"}]},"article_number":"25","oa":1,"year":"2020","intvolume":" 4","publisher":"ACM","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-01T00:00:00Z","external_id":{"arxiv":["1902.04744"]},"scopus_import":"1","date_created":"2020-08-30T22:01:12Z","publication_identifier":{"eissn":["2475-1421"]},"project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","status":"public","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","author":[{"first_name":"Peixin","last_name":"Wang","full_name":"Wang, Peixin"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Deng","full_name":"Deng, Yuxin","first_name":"Yuxin"},{"last_name":"Xu","full_name":"Xu, Ming","first_name":"Ming"}],"title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","_id":"8324","issue":"POPL","abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"doi":"10.1145/3371093","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"file_id":"8328","date_created":"2020-09-01T11:12:58Z","file_name":"2019_ACM_POPL_Wang.pdf","creator":"cziletti","relation":"main_file","file_size":564151,"access_level":"open_access","content_type":"application/pdf","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"date_updated":"2020-09-01T11:12:58Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":4,"day":"01","citation":{"chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093"},"file_date_updated":"2020-09-01T11:12:58Z","ddc":["004"],"month":"01","oa_version":"Published Version"},{"year":"2020","oa":1,"page":"1649-1675","article_type":"original","date_updated":"2023-08-22T09:00:03Z","publication":"Communications in Mathematical Physics","date_created":"2020-08-30T22:01:13Z","scopus_import":"1","external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"date_published":"2020-09-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1711.04285","open_access":"1"}],"intvolume":" 378","doi":"10.1007/s00220-020-03828-8","abstract":[{"lang":"eng","text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. "}],"issue":"9","_id":"8325","title":"Sandpile solitons via smoothing of superharmonic functions","author":[{"first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-4310-178X"}],"ec_funded":1,"publication_status":"published","acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","status":"public","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"oa_version":"Preprint","month":"09","citation":{"apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8."},"day":"01","article_processing_charge":"No","volume":378,"arxiv":1},{"date_published":"2020-12-14T00:00:00Z","external_id":{"isi":["000576148700001"]},"scopus_import":"1","date_created":"2020-09-03T16:10:56Z","department":[{"_id":"StFr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":" 59","main_file_link":[{"url":"https://doi.org/10.1002/anie.202008253","open_access":"1"}],"publisher":"Wiley","year":"2020","oa":1,"related_material":{"record":[{"id":"9780","relation":"research_data","status":"public"}]},"article_type":"original","page":"22943-22946","publication":"Angewandte Chemie International Edition","date_updated":"2023-09-05T16:03:47Z","oa_version":"Published Version","day":"14","citation":{"chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253.","mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","ieee":"W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946."},"month":"12","volume":59,"article_processing_charge":"No","issue":"51","abstract":[{"lang":"eng","text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles."}],"doi":"10.1002/anie.202008253","author":[{"first_name":"Werner","full_name":"Schlemmer, Werner","last_name":"Schlemmer"},{"full_name":"Nothdurft, Philipp","last_name":"Nothdurft","first_name":"Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"first_name":"Philipp","full_name":"Frühwirt, Philipp","last_name":"Frühwirt"},{"first_name":"Max","full_name":"Schmallegger, Max","last_name":"Schmallegger"},{"first_name":"Georg","full_name":"Gescheidt-Demner, Georg","last_name":"Gescheidt-Demner"},{"first_name":"Roland","full_name":"Fischer, Roland","last_name":"Fischer"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Wolfgang","full_name":"Kern, Wolfgang","last_name":"Kern"},{"full_name":"Spirk, Stefan","last_name":"Spirk","first_name":"Stefan"}],"title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","_id":"8329","publication_status":"published","acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","status":"public","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"date_created":"2020-09-04T12:24:12Z","date_published":"2020-09-03T00:00:00Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"alternative_title":["ISTA Thesis"],"year":"2020","date_updated":"2023-09-13T08:45:08Z","page":"120","related_material":{"record":[{"id":"133","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"status":"public","relation":"part_of_dissertation","id":"8195"},{"id":"160","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2020-09-04T13:00:17Z","month":"09","ddc":["000"],"citation":{"ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332."},"day":"03","oa_version":"Published Version","file":[{"date_created":"2020-09-04T12:17:47Z","file_id":"8333","content_type":"application/pdf","checksum":"26fe261550f691280bda4c454bf015c7","access_level":"open_access","date_updated":"2020-09-04T12:17:47Z","relation":"main_file","file_size":1348815,"creator":"bkragl","file_name":"kragl-thesis.pdf"},{"date_updated":"2020-09-04T13:00:17Z","content_type":"application/zip","checksum":"b9694ce092b7c55557122adba8337ebc","access_level":"closed","relation":"source_file","creator":"bkragl","file_size":372312,"file_name":"kragl-thesis.zip","date_created":"2020-09-04T13:00:17Z","file_id":"8335"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"8332","supervisor":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"}],"doi":"10.15479/AT:ISTA:8332","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published"},{"ec_funded":1,"publication_status":"published","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-020-17949-0","abstract":[{"text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.","lang":"eng"}],"_id":"8336","author":[{"id":"946011F4-3E71-11EA-860B-C7A73DDC885E","first_name":"Karolina","full_name":"Kubiasova, Karolina","last_name":"Kubiasova","orcid":"0000-0001-5630-9419"},{"orcid":"0000-0001-9179-6099","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","full_name":"Šamajová, Olga","last_name":"Šamajová"},{"full_name":"Nisler, Jaroslav","last_name":"Nisler","first_name":"Jaroslav"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","full_name":"Semeradova, Hana"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Marhavý, Peter","last_name":"Marhavý","orcid":"0000-0001-5227-5741"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"full_name":"Zalabák, David","last_name":"Zalabák","first_name":"David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"first_name":"Petr","last_name":"Galuszka","full_name":"Galuszka, Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"last_name":"Spíchal","full_name":"Spíchal, Lukáš","first_name":"Lukáš"}],"title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","volume":11,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2020-09-10T08:05:19Z","file_id":"8357","creator":"dernst","file_size":3455704,"relation":"main_file","file_name":"2020_NatureComm_Kubiasova.pdf","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-09-10T08:05:19Z","success":1}],"oa_version":"Published Version","ddc":["580"],"file_date_updated":"2020-09-10T08:05:19Z","month":"08","pmid":1,"day":"27","citation":{"ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0."},"article_type":"original","article_number":"4285","date_updated":"2023-08-22T09:09:06Z","publication":"Nature Communications","year":"2020","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":" 11","publisher":"Springer Nature","scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2020-09-06T22:01:12Z","date_published":"2020-08-27T00:00:00Z","external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EvBe"}]}]