[{"citation":{"chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Jonna","full_name":"Kulmuni, Jonna","last_name":"Kulmuni"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."},{"last_name":"Lucek","full_name":"Lucek, Kay","first_name":"Kay"},{"last_name":"Savolainen","full_name":"Savolainen, Vincent","first_name":"Vincent"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"}],"external_id":{"pmid":["32654637"],"isi":["000552662100001"]},"article_processing_charge":"No","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","article_number":"20190528","project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"year":"2020","day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","date_published":"2020-07-12T00:00:00Z","doi":"10.1098/rstb.2019.0528","date_created":"2020-07-26T22:01:01Z","quality_controlled":"1","publisher":"The Royal Society","oa":1,"date_updated":"2023-08-22T08:21:31Z","department":[{"_id":"NiBa"}],"_id":"8168","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1806","volume":375,"ec_funded":1,"abstract":[{"lang":"eng","text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0528","open_access":"1"}],"month":"07","intvolume":" 375"},{"article_type":"original","type":"journal_article","status":"public","_id":"8167","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T08:22:13Z","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"scopus_import":"1","intvolume":" 375","month":"07","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"pmid":1,"oa_version":"Published Version","issue":"1806","volume":375,"publication_status":"published","publication_identifier":{"eissn":["1471-2970"]},"language":[{"iso":"eng"}],"article_number":"20190545","article_processing_charge":"No","external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"last_name":"Eyres","full_name":"Eyres, Isobel","first_name":"Isobel"},{"last_name":"Broquet","full_name":"Broquet, Thomas","first_name":"Thomas"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"title":"The evolution of strong reproductive isolation between sympatric intertidal snails","citation":{"ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"The Royal Society","acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","date_created":"2020-07-26T22:01:01Z","doi":"10.1098/rstb.2019.0545","date_published":"2020-07-12T00:00:00Z","year":"2020","isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","day":"12"},{"department":[{"_id":"MiLe"}],"date_updated":"2023-08-22T08:22:43Z","article_type":"original","type":"journal_article","status":"public","_id":"8170","ec_funded":1,"issue":"1","volume":125,"publication_status":"published","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.02694"}],"scopus_import":"1","intvolume":" 125","month":"07","abstract":[{"lang":"eng","text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes."}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"author":[{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"first_name":"Lars","last_name":"Christiansen","full_name":"Christiansen, Lars"},{"last_name":"Schouder","full_name":"Schouder, Constant A.","first_name":"Constant A."},{"full_name":"Jørgensen, Anders V.","last_name":"Jørgensen","first_name":"Anders V."},{"first_name":"Benjamin","full_name":"Shepperson, Benjamin","last_name":"Shepperson"},{"first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"first_name":"Robert E.","last_name":"Zillich","full_name":"Zillich, Robert E."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik","first_name":"Henrik"}],"title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","citation":{"mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ieee":"A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020.","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","name":"A path-integral approach to composite impurities"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"013001","date_created":"2020-07-26T22:01:02Z","date_published":"2020-07-03T00:00:00Z","doi":"10.1103/PhysRevLett.125.013001","year":"2020","isi":1,"publication":"Physical Review Letters","day":"03","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University."},{"department":[{"_id":"ToHe"}],"date_updated":"2023-08-22T08:27:25Z","type":"conference","conference":{"end_date":"2020-07-04","location":"Paris, France","start_date":"2020-07-01","name":"IJCAR: International Joint Conference on Automated Reasoning"},"status":"public","_id":"8194","volume":12166,"publication_identifier":{"eissn":["16113349"],"isbn":["9783030510732"],"issn":["03029743"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://doi.org/10.1007/978-3-030-51074-9_2","open_access":"1"}],"month":"06","intvolume":" 12166","abstract":[{"text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.","lang":"eng"}],"oa_version":"Published Version","author":[{"last_name":"Baranowski","full_name":"Baranowski, Marek","first_name":"Marek"},{"last_name":"He","full_name":"He, Shaobo","first_name":"Shaobo"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Nguyen","full_name":"Nguyen, Thanh Son","first_name":"Thanh Son"},{"first_name":"Zvonimir","full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić"}],"article_processing_charge":"No","external_id":{"isi":["000884318000002"]},"title":"An SMT theory of fixed-point arithmetic","citation":{"ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"page":"13-31","date_published":"2020-06-24T00:00:00Z","doi":"10.1007/978-3-030-51074-9_2","date_created":"2020-08-02T22:00:59Z","isi":1,"year":"2020","day":"24","publication":"Automated Reasoning","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"status":"public","type":"journal_article","article_type":"original","_id":"8169","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T08:23:24Z","month":"07","intvolume":" 375","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"issue":"1806","volume":375,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14712970"]},"publication_status":"published","article_number":"20190544","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","author":[{"first_name":"Huiying","full_name":"Shang, Huiying","last_name":"Shang"},{"last_name":"Hess","full_name":"Hess, Jaqueline","first_name":"Jaqueline"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"first_name":"Pär K.","full_name":"Ingvarsson, Pär K.","last_name":"Ingvarsson"},{"last_name":"Liu","full_name":"Liu, Jianquan","first_name":"Jianquan"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"}],"external_id":{"pmid":["32654641"],"isi":["000552662100013"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544."},"quality_controlled":"1","publisher":"The Royal Society","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","doi":"10.1098/rstb.2019.0544","date_published":"2020-07-12T00:00:00Z","date_created":"2020-07-26T22:01:02Z","day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","isi":1,"year":"2020"},{"isi":1,"year":"2020","day":"01","publication":"Nano Energy","date_published":"2020-11-01T00:00:00Z","doi":"10.1016/j.nanoen.2020.105116","date_created":"2020-08-02T22:00:57Z","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","quality_controlled":"1","publisher":"Elsevier","citation":{"ieee":"X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116","mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020, doi:10.1016/j.nanoen.2020.105116.","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Yu, Xiaoting","last_name":"Yu","first_name":"Xiaoting"},{"first_name":"Junfeng","full_name":"Liu, Junfeng","last_name":"Liu"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"last_name":"Luo","full_name":"Luo, Zhishan","first_name":"Zhishan"},{"first_name":"Yong","full_name":"Zuo, Yong","last_name":"Zuo"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"last_name":"Llorca","full_name":"Llorca, Jordi","first_name":"Jordi"},{"first_name":"Déspina","last_name":"Nasiou","full_name":"Nasiou, Déspina"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"last_name":"Pan","full_name":"Pan, Kai","first_name":"Kai"},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"first_name":"Ying","last_name":"Xie","full_name":"Xie, Ying"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"article_processing_charge":"No","external_id":{"isi":["000581738300030"]},"title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","article_number":"105116","publication_identifier":{"issn":["2211-2855"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"11","volume":77,"abstract":[{"lang":"eng","text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface."}],"oa_version":"None","scopus_import":"1","month":"11","intvolume":" 77","date_updated":"2023-08-22T08:24:05Z","department":[{"_id":"MaIb"}],"_id":"8189","article_type":"original","type":"journal_article","status":"public"},{"month":"07","intvolume":" 117","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"issue":"29","volume":117,"ec_funded":1,"file":[{"file_id":"8223","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","creator":"dernst","date_updated":"2020-08-10T06:50:28Z","file_size":1111604}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10916490"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8220","department":[{"_id":"EdHa"}],"file_date_updated":"2020-08-10T06:50:28Z","ddc":["570"],"date_updated":"2023-08-22T08:29:30Z","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","doi":"10.1073/pnas.1921205117","date_published":"2020-07-21T00:00:00Z","date_created":"2020-08-09T22:00:52Z","page":"16969-16975","day":"21","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","isi":1,"year":"2020","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"title":"Stem cell lineage survival as a noisy competition for niche access","author":[{"last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."},{"last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek","first_name":"Saskia I.J."},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"first_name":"Jacco","full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020."}},{"ec_funded":1,"volume":9,"publication_status":"published","publication_identifier":{"issn":["2542-4653"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8202","file_size":531137,"date_updated":"2020-08-06T08:56:06Z","creator":"dernst","file_name":"2020_SciPostPhys_Gulden.pdf","date_created":"2020-08-06T08:56:06Z"}],"scopus_import":"1","intvolume":" 9","month":"07","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MaSe"}],"file_date_updated":"2020-08-06T08:56:06Z","date_updated":"2023-08-22T08:28:24Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8199","date_created":"2020-08-04T13:04:15Z","doi":"10.21468/scipostphys.9.1.015","date_published":"2020-07-29T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"SciPost Physics","day":"29","oa":1,"publisher":"SciPost Foundation","quality_controlled":"1","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","article_processing_charge":"No","external_id":{"isi":["000557362300008"]},"author":[{"last_name":"Gulden","full_name":"Gulden, Tobias","orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","first_name":"Tobias"},{"first_name":"Erez","full_name":"Berg, Erez","last_name":"Berg"},{"last_name":"Rudner","full_name":"Rudner, Mark Spencer","first_name":"Mark Spencer"},{"full_name":"Lindner, Netanel","last_name":"Lindner","first_name":"Netanel"}],"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","citation":{"chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020.","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"015"},{"_id":"8261","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-08-22T08:30:55Z","ddc":["570"],"file_date_updated":"2020-12-04T09:29:21Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"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."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"oa_version":"Published Version","pmid":1,"month":"09","intvolume":" 107","publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","file":[{"success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_id":"8920","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Neuron_Zhang.pdf","date_created":"2020-12-04T09:29:21Z","file_size":3011120,"date_updated":"2020-12-04T09:29:21Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":107,"issue":"6","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","relation":"press_release","description":"News on IST Website"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"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.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"article_processing_charge":"No","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","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.","quality_controlled":"1","publisher":"Elsevier","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"23","publication":"Neuron","page":"1212-1225","doi":"10.1016/j.neuron.2020.07.006","date_published":"2020-09-23T00:00:00Z","date_created":"2020-08-14T09:36:05Z"},{"publication_status":"published","publication_identifier":{"issn":["1053587X"],"eissn":["19410476"]},"language":[{"iso":"eng"}],"volume":68,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.04907"}],"scopus_import":"1","intvolume":" 68","month":"07","date_updated":"2023-08-22T08:40:08Z","department":[{"_id":"DaAl"}],"_id":"8268","article_type":"original","type":"journal_article","status":"public","year":"2020","isi":1,"publication":"IEEE Transactions on Signal Processing","day":"20","page":"4268-4282","date_created":"2020-08-16T22:00:56Z","date_published":"2020-07-20T00:00:00Z","doi":"10.1109/TSP.2020.3010355","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.","oa":1,"quality_controlled":"1","publisher":"IEEE","citation":{"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.","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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1802.04907"],"isi":["000562044500001"]},"article_processing_charge":"No","author":[{"full_name":"Gurel, Nezihe Merve","last_name":"Gurel","first_name":"Nezihe Merve"},{"first_name":"Kaan","full_name":"Kara, Kaan","last_name":"Kara"},{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"last_name":"Smith","full_name":"Smith, Tyler","first_name":"Tyler"},{"first_name":"Thomas","full_name":"Lemmin, Thomas","last_name":"Lemmin"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","last_name":"Puschel","full_name":"Puschel, Markus"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"publication_status":"published","issue":"9","volume":13,"oa_version":"None","pmid":1,"month":"09","intvolume":" 13","scopus_import":"1","date_updated":"2023-08-22T08:40:35Z","department":[{"_id":"JiFr"}],"_id":"8271","status":"public","article_type":"original","type":"journal_article","day":"07","publication":"Molecular Plant","isi":1,"year":"2020","date_published":"2020-09-07T00:00:00Z","doi":"10.1016/j.molp.2020.07.006","date_created":"2020-08-16T22:00:57Z","page":"1238-1240","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.","quality_controlled":"1","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","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","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","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."},"title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","author":[{"full_name":"He, Peng","last_name":"He","first_name":"Peng"},{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"first_name":"Guanghui","full_name":"Xiao, Guanghui","last_name":"Xiao"}],"external_id":{"isi":["000566895400007"],"pmid":["32688032"]},"article_processing_charge":"No"},{"article_number":"082602","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"isi":["000561897000001"],"arxiv":["2006.07120"]},"author":[{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","last_name":"Grosjean","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M"},{"full_name":"Wald, Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian"},{"first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"title":"Quantitatively consistent scale-spanning model for same-material tribocharging","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2020","has_accepted_license":"1","isi":1,"publication":"Physical Review Materials","day":"17","date_created":"2020-07-07T11:33:54Z","date_published":"2020-08-17T00:00:00Z","doi":"10.1103/PhysRevMaterials.4.082602","_id":"8101","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"status":"public","date_updated":"2023-08-22T08:41:32Z","ddc":["530"],"department":[{"_id":"ScWa"}],"file_date_updated":"2020-08-17T15:54:20Z","abstract":[{"lang":"eng","text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 4","month":"08","publication_status":"published","publication_identifier":{"issn":["2475-9953"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8277","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Grosjean2020.pdf","date_created":"2020-08-17T15:54:20Z","file_size":853753,"date_updated":"2020-08-17T15:54:20Z","creator":"ggrosjea"}],"ec_funded":1,"issue":"8","related_material":{"record":[{"relation":"popular_science","status":"public","id":"12697"}]},"volume":4},{"status":"public","article_type":"original","type":"journal_article","_id":"8325","department":[{"_id":"TaHa"}],"date_updated":"2023-08-22T09:00:03Z","intvolume":" 378","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1711.04285","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","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. "}],"ec_funded":1,"volume":378,"issue":"9","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Sandpile solitons via smoothing of superharmonic functions","article_processing_charge":"No","external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"author":[{"first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","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.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","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","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"},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","date_created":"2020-08-30T22:01:13Z","doi":"10.1007/s00220-020-03828-8","date_published":"2020-09-01T00:00:00Z","page":"1649-1675","publication":"Communications in Mathematical Physics","day":"01","year":"2020","isi":1},{"article_number":"4135","article_processing_charge":"No","external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"author":[{"last_name":"Gutierrez-Fernandez","full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier"},{"last_name":"Kaszuba","full_name":"Kaszuba, Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol"},{"first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S.","last_name":"Minhas"},{"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.","last_name":"Gallagher","full_name":"Gallagher, David T."},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Key role of quinone in the mechanism of respiratory complex I","citation":{"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.","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","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","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.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","date_created":"2020-08-30T22:01:10Z","date_published":"2020-08-18T00:00:00Z","doi":"10.1038/s41467-020-17957-0","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8318","file_date_updated":"2020-08-31T13:40:00Z","department":[{"_id":"LeSa"}],"date_updated":"2023-08-22T09:03:00Z","ddc":["570"],"scopus_import":"1","intvolume":" 11","month":"08","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_version":"Published Version","pmid":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}]},"volume":11,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-08-31T13:40:00Z","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","creator":"cziletti","date_updated":"2020-08-31T13:40:00Z","file_size":7527373,"checksum":"52b96f41d7d0db9728064c08da00d030","file_id":"8326","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T09:01:03Z","article_type":"original","type":"journal_article","status":"public","_id":"8320","issue":"4","related_material":{"record":[{"status":"public","id":"8321","relation":"original"}]},"volume":54,"publication_status":"published","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 54","month":"08","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."}],"oa_version":"None","external_id":{"isi":["000562110300001"]},"article_processing_charge":"No","author":[{"first_name":"S. A.","full_name":"Mukba, S. A.","last_name":"Mukba"},{"last_name":"Vlasov","full_name":"Vlasov, Petr","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."}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","citation":{"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.","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.","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","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","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.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"475-484","date_created":"2020-08-30T22:01:11Z","doi":"10.1134/S0026893320040111","date_published":"2020-08-19T00:00:00Z","year":"2020","isi":1,"publication":"Molecular Biology","day":"19","quality_controlled":"1","publisher":"Springer Nature","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."},{"related_material":{"record":[{"status":"public","id":"8320","relation":"translation"}]},"volume":54,"issue":"4","publication_status":"published","publication_identifier":{"issn":["00268984"]},"language":[{"iso":"rus"}],"scopus_import":"1","intvolume":" 54","month":"07","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."}],"pmid":1,"oa_version":"None","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T09:01:02Z","article_type":"original","type":"journal_article","status":"public","_id":"8321","page":"531-541","date_created":"2020-08-30T22:01:11Z","date_published":"2020-07-01T00:00:00Z","doi":"10.31857/S0026898420040126","year":"2020","publication":"Molekuliarnaia biologiia","day":"01","publisher":"Russian Academy of Sciences","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["32799218"]},"author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"last_name":"Shuvalova","full_name":"Shuvalova, E. Y.","first_name":"E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","citation":{"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.","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.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","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.","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","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","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."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"publisher":"Springer Nature","oa":1,"day":"01","publication":"Discrete and Computational Geometry","isi":1,"year":"2020","date_published":"2020-10-01T00:00:00Z","doi":"10.1007/s00454-020-00237-5","date_created":"2020-08-30T22:01:12Z","page":"571-574","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","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.","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","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574."},"title":"A farewell to Ricky Pollack","author":[{"last_name":"Pach","full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János"}],"article_processing_charge":"No","external_id":{"isi":["000561483500001"]},"oa_version":"None","month":"10","intvolume":" 64","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"publication_status":"published","volume":64,"_id":"8323","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-08-22T09:05:04Z","department":[{"_id":"HeEd"}]},{"file_date_updated":"2020-09-10T08:05:19Z","department":[{"_id":"EvBe"}],"ddc":["580"],"date_updated":"2023-08-22T09:09:06Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8336","volume":11,"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-09-10T08:05:19Z","file_size":3455704,"date_created":"2020-09-10T08:05:19Z","file_name":"2020_NatureComm_Kubiasova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","file_id":"8357","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","month":"08","intvolume":" 11","scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","author":[{"last_name":"Kubiasova","full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","first_name":"Karolina"},{"last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"last_name":"Šamajová","full_name":"Šamajová, Olga","first_name":"Olga"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"last_name":"Mik","full_name":"Mik, Václav","first_name":"Václav"},{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","full_name":"Semeradova, Hana","last_name":"Semeradova"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavý, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavý"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"first_name":"David","full_name":"Zalabák, David","last_name":"Zalabák"},{"last_name":"Berka","full_name":"Berka, Karel","first_name":"Karel"},{"last_name":"Doležal","full_name":"Doležal, Karel","first_name":"Karel"},{"last_name":"Galuszka","full_name":"Galuszka, Petr","first_name":"Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"last_name":"Spíchal","full_name":"Spíchal, Lukáš","first_name":"Lukáš"}],"external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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).","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."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","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"}],"article_number":"4285","doi":"10.1038/s41467-020-17949-0","date_published":"2020-08-27T00:00:00Z","date_created":"2020-09-06T22:01:12Z","day":"27","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.)."},{"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_number":"4284","title":"Cell-surface receptors enable perception of extracellular cytokinins","author":[{"first_name":"Ioanna","last_name":"Antoniadi","full_name":"Antoniadi, Ioanna"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"full_name":"Simerský, Radim","last_name":"Simerský","first_name":"Radim"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"last_name":"Vain","full_name":"Vain, Thomas","first_name":"Thomas"},{"full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí","first_name":"Eduardo"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"full_name":"Plačková, Lenka","last_name":"Plačková","first_name":"Lenka"},{"first_name":"Korawit","last_name":"Opassathian","full_name":"Opassathian, Korawit"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"full_name":"Turnbull, Colin","last_name":"Turnbull","first_name":"Colin"}],"external_id":{"isi":["000567931000001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9.","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","doi":"10.1038/s41467-020-17700-9","date_published":"2020-08-27T00:00:00Z","date_created":"2020-09-06T22:01:13Z","day":"27","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8337","file_date_updated":"2020-12-10T12:23:56Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-08-22T09:10:32Z","month":"08","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses."}],"volume":11,"ec_funded":1,"file":[{"file_name":"2020_NatureComm_Antoniadi.pdf","date_created":"2020-12-10T12:23:56Z","creator":"dernst","file_size":3526415,"date_updated":"2020-12-10T12:23:56Z","success":1,"checksum":"5b96f39b598de7510cfefefb819b9a6d","file_id":"8936","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published"},{"page":"63","doi":"10.15479/AT:ISTA:8067","date_published":"2020-07-01T00:00:00Z","date_created":"2020-06-30T07:37:39Z","has_accepted_license":"1","year":"2020","day":"01","publisher":"IST Austria","oa":1,"author":[{"last_name":"Varzi","full_name":"Varzi, Alberto","first_name":"Alberto"},{"first_name":"Katharina","last_name":"Thanner","full_name":"Thanner, Katharina"},{"last_name":"Scipioni","full_name":"Scipioni, Roberto","first_name":"Roberto"},{"first_name":"Daniele","full_name":"Di Lecce, Daniele","last_name":"Di Lecce"},{"first_name":"Jusef","last_name":"Hassoun","full_name":"Hassoun, Jusef"},{"full_name":"Dörfler, Susanne","last_name":"Dörfler","first_name":"Susanne"},{"first_name":"Holger","full_name":"Altheus, Holger","last_name":"Altheus"},{"full_name":"Kaskel, Stefan","last_name":"Kaskel","first_name":"Stefan"},{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"}],"article_processing_charge":"No","title":"Current status and future perspectives of Lithium metal batteries","citation":{"chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067.","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p.","mla":"Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067.","ieee":"A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067","ama":"Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"8361","relation":"later_version"}]},"publication_identifier":{"issn":["2664-1690"]},"publication_status":"submitted","file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:08Z","file_size":2612498,"date_created":"2020-07-02T07:36:04Z","file_name":"20200612_JPS_review_Li_metal_submitted.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8076","checksum":"d183ca1465a1cbb4f8db27875cd156f7"}],"language":[{"iso":"eng"}],"alternative_title":["IST Austria Technical Report"],"month":"07","abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"oa_version":"Published Version","department":[{"_id":"StFr"}],"file_date_updated":"2020-07-14T12:48:08Z","date_updated":"2023-08-22T09:20:36Z","ddc":["540"],"type":"technical_report","status":"public","keyword":["Battery","Lithium metal","Lithium-sulphur","Lithium-air","All-solid-state"],"_id":"8067"},{"article_number":"228803","title":"Current status and future perspectives of lithium metal batteries","article_processing_charge":"No","external_id":{"isi":["000593857300001"]},"author":[{"last_name":"Varzi","orcid":"0000-0001-5069-0589","full_name":"Varzi, Alberto","first_name":"Alberto"},{"first_name":"Katharina","full_name":"Thanner, Katharina","orcid":"0000-0001-5394-2323","last_name":"Thanner"},{"first_name":"Roberto","orcid":"0000-0003-1926-421X","full_name":"Scipioni, Roberto","last_name":"Scipioni"},{"first_name":"Daniele","full_name":"Di Lecce, Daniele","last_name":"Di Lecce"},{"last_name":"Hassoun","full_name":"Hassoun, Jusef","first_name":"Jusef"},{"last_name":"Dörfler","full_name":"Dörfler, Susanne","first_name":"Susanne"},{"first_name":"Holger","last_name":"Altheus","full_name":"Altheus, Holger"},{"last_name":"Kaskel","full_name":"Kaskel, Stefan","first_name":"Stefan"},{"full_name":"Prehal, Christian","orcid":"0000-0003-0654-0940","last_name":"Prehal","first_name":"Christian"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803.","ieee":"A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020).","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","date_created":"2020-09-10T10:48:40Z","date_published":"2020-12-31T00:00:00Z","doi":"10.1016/j.jpowsour.2020.228803","publication":"Journal of Power Sources","day":"31","year":"2020","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"8361","department":[{"_id":"StFr"}],"date_updated":"2023-08-22T09:20:37Z","intvolume":" 480","month":"12","main_file_link":[{"url":"https://doi.org/10.1016/j.jpowsour.2020.228803","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.","lang":"eng"}],"related_material":{"record":[{"id":"8067","status":"public","relation":"earlier_version"}]},"issue":"12","volume":480,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0378-7753"]}},{"department":[{"_id":"JoFi"}],"file_date_updated":"2020-09-18T13:02:37Z","ddc":["530"],"date_updated":"2023-08-22T09:27:12Z","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8529","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","description":"News on IST Homepage"}],"record":[{"relation":"research_data","id":"13056","status":"public"}]},"volume":11,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8530","checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"date_updated":"2020-09-18T13:02:37Z","creator":"dernst","file_name":"2020_NatureComm_Arnold.pdf","date_created":"2020-09-18T13:02:37Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","month":"09","intvolume":" 11","oa_version":"Published Version","abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000577280200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z"},"project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"article_number":"4460","date_published":"2020-09-08T00:00:00Z","doi":"10.1038/s41467-020-18269-z","date_created":"2020-09-18T10:56:20Z","day":"08","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET)."},{"month":"07","intvolume":" 39","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.","lang":"eng"}],"volume":39,"issue":"4","ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-09-21T07:51:44Z","file_size":20223953,"date_created":"2020-09-21T07:51:44Z","file_name":"2020_ACM_Skrivan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_id":"8541","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"8535","file_date_updated":"2020-09-21T07:51:44Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2023-08-22T09:28:27Z","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","doi":"10.1145/3386569.3392466","date_published":"2020-07-08T00:00:00Z","date_created":"2020-09-20T22:01:37Z","day":"08","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2020","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_number":"65","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","author":[{"full_name":"Skrivan, Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Andreas","full_name":"Soderstrom, Andreas","last_name":"Soderstrom"},{"full_name":"Johansson, John","last_name":"Johansson","first_name":"John"},{"last_name":"Sprenger","full_name":"Sprenger, Christoph","first_name":"Christoph"},{"full_name":"Museth, Ken","last_name":"Museth","first_name":"Ken"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"article_processing_charge":"No","external_id":{"isi":["000583700300038"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65."}},{"abstract":[{"lang":"eng","text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions."},{"lang":"fre","text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. "}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"month":"06","intvolume":" 53","publication_identifier":{"issn":["0012-9593"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":53,"issue":"3","_id":"8539","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T09:27:57Z","department":[{"_id":"TaHa"}],"quality_controlled":"1","publisher":"Société Mathématique de France","oa":1,"isi":1,"year":"2020","day":"01","publication":"Annales Scientifiques de l'Ecole Normale Superieure","page":"663-671","doi":"10.24033/asens.2431","date_published":"2020-06-01T00:00:00Z","date_created":"2020-09-20T22:01:38Z","citation":{"mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431","apa":"Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"C.","last_name":"Su","full_name":"Su, C."},{"full_name":"Zhao, Gufang","last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang"},{"first_name":"C.","full_name":"Zhong, C.","last_name":"Zhong"}],"article_processing_charge":"No","external_id":{"isi":["000592182600004"],"arxiv":["1708.08013"]},"title":"On the K-theory stable bases of the springer resolution"},{"_id":"13056","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","citation":{"ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561."},"date_updated":"2023-08-22T09:27:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_processing_charge":"No","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3961562"}],"publisher":"Zenodo","month":"07","year":"2020","day":"27","date_created":"2023-05-23T13:37:41Z","related_material":{"record":[{"relation":"used_in_publication","id":"8529","status":"public"}]},"date_published":"2020-07-27T00:00:00Z","doi":"10.5281/ZENODO.3961561"},{"oa":1,"publisher":"MDPI","quality_controlled":"1","date_created":"2020-09-28T08:59:26Z","doi":"10.3390/membranes10090242","date_published":"2020-09-01T00:00:00Z","publication":"Membranes","day":"01","year":"2020","isi":1,"has_accepted_license":"1","article_number":"242","title":"Cu homeostasis in bacteria: The ins and outs","external_id":{"isi":["000581446000001"]},"article_processing_charge":"No","author":[{"first_name":"Andreea","full_name":"Andrei, Andreea","last_name":"Andrei"},{"first_name":"Yavuz","full_name":"Öztürk, Yavuz","last_name":"Öztürk"},{"first_name":"Bahia","last_name":"Khalfaoui-Hassani","full_name":"Khalfaoui-Hassani, Bahia"},{"first_name":"Juna","last_name":"Rauch","full_name":"Rauch, Juna"},{"full_name":"Marckmann, Dorian","last_name":"Marckmann","first_name":"Dorian"},{"id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Petru Iulian","last_name":"Trasnea","full_name":"Trasnea, Petru Iulian"},{"last_name":"Daldal","full_name":"Daldal, Fevzi","first_name":"Fevzi"},{"last_name":"Koch","full_name":"Koch, Hans-Georg","first_name":"Hans-Georg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","ieee":"A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242."},"intvolume":" 10","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"issue":"9","volume":10,"language":[{"iso":"eng"}],"file":[{"file_id":"8583","checksum":"ceb43d7554e712dea6f36f9287271737","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-28T11:36:50Z","file_name":"2020_Membranes_Andrei.pdf","creator":"dernst","date_updated":"2020-09-28T11:36:50Z","file_size":4612258}],"publication_status":"published","publication_identifier":{"eissn":["20770375"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8579","file_date_updated":"2020-09-28T11:36:50Z","department":[{"_id":"LeSa"}],"ddc":["570"],"date_updated":"2023-08-22T09:34:06Z"},{"scopus_import":"1","month":"11","intvolume":" 27","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"abstract":[{"text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.","lang":"eng"}],"oa_version":"None","pmid":1,"issue":"11","volume":27,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"publication_identifier":{"issn":["15459993"],"eissn":["15459985"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8581","department":[{"_id":"LeSa"}],"date_updated":"2023-08-22T09:33:09Z","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission.","page":"1077-1085","doi":"10.1038/s41594-020-0503-8","date_published":"2020-11-01T00:00:00Z","date_created":"2020-09-28T08:59:27Z","isi":1,"year":"2020","day":"01","publication":"Nature Structural and Molecular Biology","author":[{"first_name":"Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","full_name":"Pinke, Gergely","last_name":"Pinke"},{"last_name":"Zhou","orcid":"0000-0002-1864-8951","full_name":"Zhou, Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","first_name":"Long"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"external_id":{"pmid":["32929284"],"isi":["000569299400004"]},"article_processing_charge":"No","title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","citation":{"mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8.","ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020.","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085. doi:10.1038/s41594-020-0503-8","apa":"Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-020-0503-8","chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.","ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054.","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054","apa":"Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054","short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020."},"date_updated":"2023-08-22T09:33:34Z","department":[{"_id":"HeEd"}],"title":"The application of persistent homology in the analysis of heart rate variability","external_id":{"isi":["000621172600045"]},"article_processing_charge":"No","author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"first_name":"Beata","last_name":"Graff","full_name":"Graff, Beata"},{"last_name":"Jablonski","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"article_number":"9158054","_id":"8580","status":"public","conference":{"start_date":"2020-07-15","location":"Pisa, Italy","end_date":"2020-07-15","name":"ESGCO: European Study Group on Cardiovascular Oscillations"},"type":"conference","publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","language":[{"iso":"eng"}],"day":"01","year":"2020","publication_status":"published","isi":1,"publication_identifier":{"isbn":["9781728157511"]},"date_created":"2020-09-28T08:59:27Z","doi":"10.1109/ESGCO49734.2020.9158054","date_published":"2020-08-01T00:00:00Z","oa_version":"None","abstract":[{"text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.","lang":"eng"}],"month":"08","publisher":"IEEE","scopus_import":"1","quality_controlled":"1"},{"issue":"21","volume":7,"ec_funded":1,"file":[{"success":1,"checksum":"92818c23ecc70e35acfa671f3cfb9909","file_id":"8938","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_AdvScience_Tian.pdf","date_created":"2020-12-10T14:07:24Z","file_size":7835833,"date_updated":"2020-12-10T14:07:24Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2198-3844"]},"publication_status":"published","month":"11","intvolume":" 7","oa_version":"Published Version","abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-12-10T14:07:24Z","ddc":["570"],"date_updated":"2023-08-22T09:53:01Z","status":"public","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8592","date_published":"2020-11-04T00:00:00Z","doi":"10.1002/advs.202001724","date_created":"2020-10-01T09:44:13Z","day":"04","publication":"Advanced Science","isi":1,"has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","author":[{"first_name":"Anhao","full_name":"Tian, Anhao","last_name":"Tian"},{"first_name":"Bo","full_name":"Kang, Bo","last_name":"Kang"},{"last_name":"Li","full_name":"Li, Baizhou","first_name":"Baizhou"},{"last_name":"Qiu","full_name":"Qiu, Biying","first_name":"Biying"},{"last_name":"Jiang","full_name":"Jiang, Wenhong","first_name":"Wenhong"},{"first_name":"Fangjie","full_name":"Shao, Fangjie","last_name":"Shao"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"first_name":"Rui","last_name":"Liu","full_name":"Liu, Rui"},{"last_name":"Cai","full_name":"Cai, Chengwei","first_name":"Chengwei"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"first_name":"Wei","last_name":"Wang","full_name":"Wang, Wei"},{"full_name":"Chen, Pengxiang","last_name":"Chen","first_name":"Pengxiang"},{"first_name":"Qinghui","full_name":"Liang, Qinghui","last_name":"Liang"},{"last_name":"Bao","full_name":"Bao, Lili","first_name":"Lili"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"first_name":"Yan","last_name":"Wang","full_name":"Wang, Yan"},{"last_name":"Shi","full_name":"Shi, Yu","first_name":"Yu"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"first_name":"Minmin","last_name":"Yang","full_name":"Yang, Minmin"},{"last_name":"Wang","full_name":"Wang, Lisha","first_name":"Lisha"},{"full_name":"Zhang, Jianmin","last_name":"Zhang","first_name":"Jianmin"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Junming","last_name":"Zhu","full_name":"Zhu, Junming"},{"first_name":"Xiuwu","full_name":"Bian, Xiuwu","last_name":"Bian"},{"last_name":"Wang","full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie"},{"full_name":"Liu, Chong","last_name":"Liu","first_name":"Chong"}],"external_id":{"isi":["000573860700001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724."},"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"article_number":"2001724"},{"article_number":"4838","citation":{"ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000573756600004"]},"article_processing_charge":"No","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","last_name":"Fitzek","first_name":"Harald"},{"last_name":"Kothleitner","full_name":"Kothleitner, Gerald","first_name":"Gerald"},{"last_name":"Presser","full_name":"Presser, Volker","first_name":"Volker"},{"last_name":"Gollas","full_name":"Gollas, Bernhard","first_name":"Bernhard"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Qamar","last_name":"Abbas","full_name":"Abbas, Qamar"}],"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"24","date_created":"2020-09-25T07:23:13Z","doi":"10.1038/s41467-020-18610-6","date_published":"2020-09-24T00:00:00Z","_id":"8568","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","date_updated":"2023-08-22T09:37:24Z","ddc":["530"],"file_date_updated":"2020-09-28T13:16:15Z","department":[{"_id":"StFr"}],"abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"oa_version":"Published Version","intvolume":" 11","month":"09","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1822469,"date_updated":"2020-09-28T13:16:15Z","file_name":"2020_NatureComm_Prehal.pdf","date_created":"2020-09-28T13:16:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8585","checksum":"eada7bc8dd16a49390137cff882ef328"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"volume":11},{"abstract":[{"text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 10","publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"file_name":"2020_ScientificReport_Deichler.pdf","date_created":"2020-10-12T12:39:10Z","file_size":3906744,"date_updated":"2020-10-12T12:39:10Z","creator":"dernst","success":1,"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","file_id":"8651","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":10,"_id":"8643","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-22T09:58:21Z","ddc":["570"],"department":[{"_id":"MaJö"}],"file_date_updated":"2020-10-12T12:39:10Z","acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Scientific Reports","doi":"10.1038/s41598-020-72848-0","date_published":"2020-10-01T00:00:00Z","date_created":"2020-10-11T22:01:14Z","article_number":"16220","citation":{"mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"first_name":"Denisse","last_name":"Carrasco","full_name":"Carrasco, Denisse"},{"full_name":"Lopez-Jury, Luciana","last_name":"Lopez-Jury","first_name":"Luciana"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"first_name":"Natalia","last_name":"Marquez","full_name":"Marquez, Natalia"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"},{"first_name":"Gonzalo","last_name":"Marin","full_name":"Marin, Gonzalo"}],"article_processing_charge":"No","external_id":{"isi":["000577142600032"]},"title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents"},{"ddc":["000","570"],"date_updated":"2023-08-22T09:57:29Z","file_date_updated":"2020-10-12T12:02:09Z","department":[{"_id":"FyKo"}],"_id":"8645","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"21d6f71839deb3b83e4a356193f72767","file_id":"8649","success":1,"creator":"dernst","date_updated":"2020-10-12T12:02:09Z","file_size":308341,"date_created":"2020-10-12T12:02:09Z","file_name":"2020_Bioinformatics_Esteban.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"publication_status":"published","volume":36,"issue":"6","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data."}],"month":"03","intvolume":" 36","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841."},"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","author":[{"first_name":"Laura A","full_name":"Esteban, Laura A","last_name":"Esteban"},{"last_name":"Lonishin","full_name":"Lonishin, Lyubov R","first_name":"Lyubov R"},{"last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M"},{"first_name":"Gregory","last_name":"Leleytner","full_name":"Leleytner, Gregory"},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S","first_name":"Natalya S"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N ","last_name":"Ivankov"}],"article_processing_charge":"No","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"project":[{"name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"15","publication":"Bioinformatics","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-03-15T00:00:00Z","doi":"10.1093/bioinformatics/btz841","date_created":"2020-10-11T22:01:14Z","page":"1960-1962","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","publisher":"Oxford Academic","quality_controlled":"1","oa":1},{"_id":"8597","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T09:53:29Z","ddc":["510","570"],"department":[{"_id":"NanoFab"}],"file_date_updated":"2020-10-05T13:53:59Z","abstract":[{"text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 17","month":"09","publication_status":"published","publication_identifier":{"eissn":["14783975"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1667111,"date_updated":"2020-10-05T13:53:59Z","file_name":"2020_PhysBio_Merrin.pdf","date_created":"2020-10-05T13:53:59Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"fec9bdd355ed349f09990faab20838a7","file_id":"8609"}],"issue":"6","volume":17,"article_number":"065005","citation":{"short":"J. Merrin, Physical Biology 17 (2020).","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db","ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000575539700001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"}],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","year":"2020","isi":1,"has_accepted_license":"1","publication":"Physical Biology","day":"23","date_created":"2020-10-04T22:01:35Z","date_published":"2020-09-23T00:00:00Z","doi":"10.1088/1478-3975/abb2db"},{"title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","external_id":{"isi":["000603428000010"],"pmid":["32976770"]},"article_processing_charge":"No","author":[{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"last_name":"Bard","full_name":"Bard, Lucie","first_name":"Lucie"},{"full_name":"Panatier, Aude","last_name":"Panatier","first_name":"Aude"},{"full_name":"Reynolds, James P.","last_name":"Reynolds","first_name":"James P."},{"full_name":"Kopach, Olga","last_name":"Kopach","first_name":"Olga"},{"last_name":"Medvedev","full_name":"Medvedev, Nikolay I.","first_name":"Nikolay I."},{"first_name":"Daniel","last_name":"Minge","full_name":"Minge, Daniel"},{"first_name":"Michel K.","full_name":"Herde, Michel K.","last_name":"Herde"},{"full_name":"Anders, Stefanie","last_name":"Anders","first_name":"Stefanie"},{"full_name":"Kraev, Igor","last_name":"Kraev","first_name":"Igor"},{"first_name":"Janosch P.","last_name":"Heller","full_name":"Heller, Janosch P."},{"first_name":"Sylvain","last_name":"Rama","full_name":"Rama, Sylvain"},{"full_name":"Zheng, Kaiyu","last_name":"Zheng","first_name":"Kaiyu"},{"first_name":"Thomas P.","full_name":"Jensen, Thomas P.","last_name":"Jensen"},{"full_name":"Sanchez-Romero, Inmaculada","last_name":"Sanchez-Romero","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Colin J.","last_name":"Jackson","full_name":"Jackson, Colin J."},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ole Petter","full_name":"Ottersen, Ole Petter","last_name":"Ottersen"},{"last_name":"Nagelhus","full_name":"Nagelhus, Erlend Arnulf","first_name":"Erlend Arnulf"},{"full_name":"Oliet, Stephane H.R.","last_name":"Oliet","first_name":"Stephane H.R."},{"first_name":"Michael G.","last_name":"Stewart","full_name":"Stewart, Michael G."},{"last_name":"Nägerl","full_name":"Nägerl, U. VAlentin","first_name":"U. VAlentin"},{"first_name":"Dmitri A. ","last_name":"Rusakov","full_name":"Rusakov, Dmitri A. "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030.","ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","date_created":"2020-10-18T22:01:38Z","doi":"10.1016/j.neuron.2020.08.030","date_published":"2020-12-09T00:00:00Z","page":"P919-936.E11","publication":"Neuron","day":"09","year":"2020","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8674","department":[{"_id":"HaJa"}],"file_date_updated":"2020-12-10T14:42:09Z","ddc":["570"],"date_updated":"2023-08-22T09:59:29Z","intvolume":" 108","month":"12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.","lang":"eng"}],"volume":108,"issue":"5","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-12-10T14:42:09Z","file_size":7518960,"date_created":"2020-12-10T14:42:09Z","file_name":"2020_Neuron_Henneberger.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"054562bb50165ef9a1f46631c1c5e36b","file_id":"8939","success":1}],"publication_status":"published","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]}},{"file_date_updated":"2020-10-14T15:16:28Z","department":[{"_id":"MiLe"}],"date_updated":"2023-08-22T09:58:46Z","ddc":["530"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8652","volume":3,"ec_funded":1,"publication_identifier":{"issn":["2399-3650"]},"publication_status":"published","file":[{"checksum":"60cd35b99f0780acffc7b6060e49ec8b","file_id":"8662","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-14T15:16:28Z","file_name":"2020_CommPhysics_Ghazaryan.pdf","creator":"dernst","date_updated":"2020-10-14T15:16:28Z","file_size":1462934}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 3","abstract":[{"text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"article_processing_charge":"Yes","external_id":{"isi":["000581681000001"]},"title":"Filtering spins by scattering from a lattice of point magnets","citation":{"mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8","ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8","chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"178","doi":"10.1038/s42005-020-00445-8","date_published":"2020-10-09T00:00:00Z","date_created":"2020-10-13T09:48:59Z","has_accepted_license":"1","isi":1,"year":"2020","day":"09","publication":"Communications Physics","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON)."},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2020-10-18T22:01:35Z","doi":"10.1038/s41467-020-18837-3","date_published":"2020-10-07T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"07","article_number":"5037","external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"article_processing_charge":"No","author":[{"last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena K.","first_name":"Magdalena K."},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Roberta","full_name":"Azzarelli, Roberta","last_name":"Azzarelli"},{"first_name":"Lemonia","last_name":"Chatzeli","full_name":"Chatzeli, Lemonia"},{"last_name":"Ikeda","full_name":"Ikeda, Tatsuro","first_name":"Tatsuro"},{"last_name":"Yoshida","full_name":"Yoshida, Shosei","first_name":"Shosei"},{"first_name":"Anna","full_name":"Philpott, Anna","last_name":"Philpott"},{"last_name":"Simons","full_name":"Simons, Benjamin D","first_name":"Benjamin D"}],"title":"Tracing the cellular basis of islet specification in mouse pancreas","citation":{"ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 11","month":"10","abstract":[{"lang":"eng","text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development."}],"pmid":1,"oa_version":"Published Version","volume":11,"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8677","checksum":"0ecc0eab72d2d50694852579611a6624","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_NatureComm_Sznurkowska.pdf","date_created":"2020-10-19T11:27:46Z","file_size":5540540,"date_updated":"2020-10-19T11:27:46Z","creator":"dernst"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8669","department":[{"_id":"EdHa"}],"file_date_updated":"2020-10-19T11:27:46Z","date_updated":"2023-08-22T10:18:17Z","ddc":["570"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001"},"title":"Abscission couples cell division to embryonic stem cell fate","author":[{"first_name":"Agathe","full_name":"Chaigne, Agathe","last_name":"Chaigne"},{"first_name":"Céline","last_name":"Labouesse","full_name":"Labouesse, Céline"},{"full_name":"White, Ian J.","last_name":"White","first_name":"Ian J."},{"first_name":"Meghan","full_name":"Agnew, Meghan","last_name":"Agnew"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Chalut, Kevin J.","last_name":"Chalut","first_name":"Kevin J."},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"article_processing_charge":"No","external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"day":"26","publication":"Developmental Cell","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-10-26T00:00:00Z","doi":"10.1016/j.devcel.2020.09.001","date_created":"2020-10-18T22:01:37Z","page":"195-208","acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","publisher":"Elsevier","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-08-22T10:16:58Z","department":[{"_id":"EdHa"}],"file_date_updated":"2021-02-04T10:20:02Z","_id":"8672","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9086","checksum":"88e1a031a61689165d19a19c2f16d795","file_size":6929686,"date_updated":"2021-02-04T10:20:02Z","creator":"dernst","file_name":"2020_DevelopmCell_Chaigne.pdf","date_created":"2021-02-04T10:20:02Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"publication_status":"published","volume":55,"issue":"2","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.","lang":"eng"}],"month":"10","intvolume":" 55","scopus_import":"1"},{"page":"5733-5772","doi":"10.1088/1361-6544/ab9728","date_published":"2020-11-01T00:00:00Z","date_created":"2020-10-25T23:01:16Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Nonlinearity","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","last_name":"Kniely","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1906.12245"],"isi":["000576492700001"]},"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","citation":{"ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":33,"issue":"11","license":"https://creativecommons.org/licenses/by/3.0/","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","file_id":"8710","creator":"cziletti","file_size":1223899,"date_updated":"2020-10-27T12:09:57Z","file_name":"2020_Nonlinearity_Fischer.pdf","date_created":"2020-10-27T12:09:57Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 33","abstract":[{"lang":"eng","text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest."}],"oa_version":"Published Version","file_date_updated":"2020-10-27T12:09:57Z","department":[{"_id":"JuFi"}],"date_updated":"2023-08-22T10:38:38Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"status":"public","_id":"8697"},{"author":[{"last_name":"Tsai","full_name":"Tsai, Tony Y.-C.","first_name":"Tony Y.-C."},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","full_name":"Xia, Peng"},{"first_name":"Tugba","last_name":"Colak-Champollion","full_name":"Colak-Champollion, Tugba"},{"first_name":"Holger","full_name":"Knaut, Holger","last_name":"Knaut"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"external_id":{"isi":["000579169000053"]},"article_processing_charge":"No","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","citation":{"mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"page":"113-116","doi":"10.1126/science.aba6637","date_published":"2020-10-02T00:00:00Z","date_created":"2020-10-19T14:09:38Z","isi":1,"year":"2020","day":"02","publication":"Science","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","department":[{"_id":"CaHe"}],"date_updated":"2023-08-22T10:36:35Z","type":"journal_article","article_type":"original","status":"public","keyword":["Multidisciplinary"],"_id":"8680","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/sticking-together/"}]},"volume":370,"issue":"6512","ec_funded":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"month":"10","intvolume":" 370","abstract":[{"lang":"eng","text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning."}],"oa_version":"Preprint"},{"volume":52,"publication_identifier":{"issn":["10614036"],"eissn":["15461718"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 52","abstract":[{"text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.","lang":"eng"}],"pmid":1,"oa_version":"None","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T10:37:10Z","article_type":"original","type":"journal_article","status":"public","_id":"8707","page":"1247-1255","doi":"10.1038/s41588-020-00712-y","date_published":"2020-10-19T00:00:00Z","date_created":"2020-10-25T23:01:20Z","isi":1,"year":"2020","day":"19","publication":"Nature Genetics","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","author":[{"first_name":"Silvia","full_name":" Galan, Silvia","last_name":" Galan"},{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N","last_name":"Machnik","orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N"},{"first_name":"Kai","last_name":"Kruse","full_name":"Kruse, Kai"},{"first_name":"Noelia","full_name":"Díaz, Noelia","last_name":"Díaz"},{"last_name":"Marti-Renom","full_name":"Marti-Renom, Marc A","first_name":"Marc A"},{"last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M","first_name":"Juan M"}],"external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"article_processing_charge":"No","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","citation":{"ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y.","short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"type":"journal_article","article_type":"original","status":"public","_id":"8679","department":[{"_id":"ToHe"}],"date_updated":"2023-08-22T10:36:06Z","scopus_import":"1","intvolume":" 2","month":"10","abstract":[{"lang":"eng","text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system."}],"oa_version":"None","volume":2,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-deep-learning-models/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","publication_identifier":{"eissn":["2522-5839"]},"language":[{"iso":"eng"}],"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000583337200011"]},"article_processing_charge":"No","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"first_name":"Alexander","full_name":"Amini, Alexander","last_name":"Amini"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"title":"Neural circuit policies enabling auditable autonomy","citation":{"ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.","ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3","mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","page":"642-652","date_created":"2020-10-19T13:46:06Z","doi":"10.1038/s42256-020-00237-3","date_published":"2020-10-01T00:00:00Z","year":"2020","isi":1,"publication":"Nature Machine Intelligence","day":"01"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06644"}],"scopus_import":"1","intvolume":" 61","month":"10","abstract":[{"lang":"eng","text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]."}],"oa_version":"Preprint","ec_funded":1,"volume":61,"issue":"10","publication_status":"published","publication_identifier":{"issn":["00222488"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8670","department":[{"_id":"JaMa"}],"date_updated":"2023-08-22T10:32:29Z","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","date_created":"2020-10-18T22:01:36Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1063/5.0022787","year":"2020","isi":1,"publication":"Journal of Mathematical Physics","day":"01","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"102201","external_id":{"arxiv":["2007.06644"],"isi":["000578529200001"]},"article_processing_charge":"No","author":[{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","citation":{"ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_status":"published","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_PNAS_Maoz.pdf","date_created":"2020-10-27T14:57:50Z","file_size":1755359,"date_updated":"2020-10-27T14:57:50Z","creator":"cziletti","success":1,"file_id":"8713","checksum":"c6a24fdecf3f28faf447078e7a274a88","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":117,"issue":"40","abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 117","month":"10","date_updated":"2023-08-22T12:11:23Z","ddc":["570"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-10-27T14:57:50Z","_id":"8698","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","year":"2020","has_accepted_license":"1","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"06","page":"25066-25073","date_created":"2020-10-25T23:01:16Z","doi":"10.1073/pnas.1912804117","date_published":"2020-10-06T00:00:00Z","acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","citation":{"mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.","apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"article_processing_charge":"No","author":[{"full_name":"Maoz, Ori","last_name":"Maoz","first_name":"Ori"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"first_name":"Mohamad Saleh","full_name":"Esteki, Mohamad Saleh","last_name":"Esteki"},{"first_name":"Roozbeh","last_name":"Kiani","full_name":"Kiani, Roozbeh"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"title":"Learning probabilistic neural representations with randomly connected circuits"},{"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1070010,"date_updated":"2020-11-06T10:58:49Z","file_name":"2020_ICRA_Lechner.pdf","date_created":"2020-11-06T10:58:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8733","checksum":"fccf7b986ac78046918a298cc6849a50"}],"publication_status":"published","publication_identifier":{"isbn":["9781728173955"],"issn":["10504729"]},"oa_version":"Submitted Version","abstract":[{"text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.","lang":"eng"}],"month":"05","scopus_import":"1","alternative_title":["ICRA"],"ddc":["000"],"date_updated":"2023-08-22T10:40:15Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-11-06T10:58:49Z","_id":"8704","status":"public","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2020-05-31","end_date":"2020-08-31","location":"Paris, France"},"type":"conference","publication":"Proceedings - IEEE International Conference on Robotics and Automation","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-10-25T23:01:19Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1109/ICRA40945.2020.9196608","page":"5446-5452","acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","oa":1,"publisher":"IEEE","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.","apa":"Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608","ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452.","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.","ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452."},"title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","article_processing_charge":"No","external_id":{"isi":["000712319503110"]},"author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","page":"739-748","date_created":"2020-10-25T23:01:17Z","date_published":"2020-09-01T00:00:00Z","doi":"10.1134/S0026893320050088","year":"2020","isi":1,"publication":"Molecular Biology","day":"01","external_id":{"isi":["000579441200009"]},"article_processing_charge":"No","author":[{"first_name":"E. E.","last_name":"Sokolova","full_name":"Sokolova, E. E."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Vlasov, Petr","last_name":"Vlasov"},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"first_name":"A. V.","last_name":"Shuvalov","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","citation":{"ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 54","month":"09","abstract":[{"text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.","lang":"eng"}],"oa_version":"None","related_material":{"record":[{"id":"8701","status":"public","relation":"original"}]},"issue":"5","volume":54,"publication_status":"published","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"8700","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T10:39:38Z"},{"language":[{"iso":"rus"}],"publication_identifier":{"issn":["00268984"]},"publication_status":"published","volume":54,"issue":"5","related_material":{"record":[{"status":"public","id":"8700","relation":"translation"}]},"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"month":"09","intvolume":" 54","scopus_import":"1","date_updated":"2023-08-22T10:39:37Z","department":[{"_id":"FyKo"}],"_id":"8701","status":"public","type":"journal_article","article_type":"original","day":"01","publication":"Molekuliarnaia biologiia","year":"2020","doi":"10.31857/S0026898420050080","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-25T23:01:17Z","page":"837-848","publisher":"Russian Academy of Sciences","quality_controlled":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080."},"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","author":[{"full_name":"Sokolova, E. E.","last_name":"Sokolova","first_name":"E. E."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"T. V.","full_name":"Egorova, T. V.","last_name":"Egorova"},{"full_name":"Shuvalov, A. V.","last_name":"Shuvalov","first_name":"A. V."},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"external_id":{"pmid":["33009793"]},"article_processing_charge":"No"},{"title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","author":[{"first_name":"Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith","full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith"},{"full_name":"Everson, Rosa Wallace","last_name":"Everson","first_name":"Rosa Wallace"},{"first_name":"Enrico Ramirez-Ruiz","full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz","last_name":"Enrico Ramirez-Ruiz"},{"full_name":"Mink, Selma E. de","last_name":"Mink","first_name":"Selma E. de"},{"last_name":"Son","full_name":"Son, Lieke A. C. van","first_name":"Lieke A. C. van"},{"orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"full_name":"Zellmann, Stefan","last_name":"Zellmann","first_name":"Stefan"},{"first_name":"Alejandro Vigna-Gómez","last_name":"Alejandro Vigna-Gómez","full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez"},{"full_name":"Renzo, Mathieu","last_name":"Renzo","first_name":"Mathieu"},{"first_name":"Samantha","full_name":"Wu, Samantha","last_name":"Wu"},{"last_name":"Schrøder","full_name":"Schrøder, Sophie L.","first_name":"Sophie L."},{"first_name":"Ryan J.","last_name":"Foley","full_name":"Foley, Ryan J."},{"first_name":"Tenley Hutchinson-Smith","full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith"}],"article_processing_charge":"No","external_id":{"arxiv":["2011.06630"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630.","ista":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630.","mla":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630.","ieee":"J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. .","short":"J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.).","ama":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630","apa":"Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630"},"date_updated":"2023-08-22T11:03:00Z","status":"public","type":"preprint","article_number":"2011.06630","_id":"14096","doi":"10.48550/arXiv.2011.06630","date_published":"2020-11-12T00:00:00Z","date_created":"2023-08-21T10:10:41Z","day":"12","language":[{"iso":"eng"}],"publication":"arXiv","publication_status":"submitted","year":"2020","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"oa_version":"Preprint","abstract":[{"text":"A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources.","lang":"eng"}]},{"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","page":"24764-24770","date_created":"2020-10-25T23:01:17Z","date_published":"2020-10-06T00:00:00Z","doi":"10.1073/pnas.2012043117","year":"2020","has_accepted_license":"1","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"06","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"isi":["000579059100029"],"pmid":["32958669"],"arxiv":["2009.12262"]},"article_processing_charge":"No","author":[{"first_name":"Eugenio","full_name":"Paris, Eugenio","last_name":"Paris"},{"last_name":"Tseng","full_name":"Tseng, Yi","first_name":"Yi"},{"full_name":"Paerschke, Ekaterina","orcid":"0000-0003-0853-8182","last_name":"Paerschke","first_name":"Ekaterina","id":"8275014E-6063-11E9-9B7F-6338E6697425"},{"first_name":"Wenliang","full_name":"Zhang, Wenliang","last_name":"Zhang"},{"full_name":"Upton, Mary H","last_name":"Upton","first_name":"Mary H"},{"full_name":"Efimenko, Anna","last_name":"Efimenko","first_name":"Anna"},{"first_name":"Katharina","full_name":"Rolfs, Katharina","last_name":"Rolfs"},{"first_name":"Daniel E","full_name":"McNally, Daniel E","last_name":"McNally"},{"full_name":"Maurel, Laura","last_name":"Maurel","first_name":"Laura"},{"full_name":"Naamneh, Muntaser","last_name":"Naamneh","first_name":"Muntaser"},{"first_name":"Marco","last_name":"Caputo","full_name":"Caputo, Marco"},{"first_name":"Vladimir N","full_name":"Strocov, Vladimir N","last_name":"Strocov"},{"full_name":"Wang, Zhiming","last_name":"Wang","first_name":"Zhiming"},{"first_name":"Diego","full_name":"Casa, Diego","last_name":"Casa"},{"first_name":"Christof W","last_name":"Schneider","full_name":"Schneider, Christof W"},{"last_name":"Pomjakushina","full_name":"Pomjakushina, Ekaterina","first_name":"Ekaterina"},{"last_name":"Wohlfeld","full_name":"Wohlfeld, Krzysztof","first_name":"Krzysztof"},{"full_name":"Radovic, Milan","last_name":"Radovic","first_name":"Milan"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","citation":{"ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 117","month":"10","abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"issue":"40","volume":117,"publication_status":"published","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"1638fa36b442e2868576c6dd7d6dc505","file_id":"8715","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PNAS_Paris.pdf","date_created":"2020-10-28T11:53:12Z","creator":"cziletti","file_size":1176522,"date_updated":"2020-10-28T11:53:12Z"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public","_id":"8699","file_date_updated":"2020-10-28T11:53:12Z","department":[{"_id":"MiLe"}],"date_updated":"2023-08-22T12:11:52Z","ddc":["530"]},{"citation":{"ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","apa":"Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209","ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["32972993"],"isi":["000583031800004"]},"author":[{"last_name":"Kampjut","full_name":"Kampjut, Domen","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"The coupling mechanism of mammalian respiratory complex I","article_number":"eabc4209","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2020","isi":1,"has_accepted_license":"1","publication":"Science","day":"30","date_created":"2020-11-08T23:01:23Z","doi":"10.1126/science.abc4209","date_published":"2020-10-30T00:00:00Z","acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","date_updated":"2023-08-22T12:35:38Z","ddc":["572"],"file_date_updated":"2020-11-26T18:47:58Z","department":[{"_id":"LeSa"}],"_id":"8737","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["10959203"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Full_manuscript_with_SI_opt_red.pdf","date_created":"2020-11-26T18:47:58Z","creator":"lsazanov","file_size":7618987,"date_updated":"2020-11-26T18:47:58Z","success":1,"file_id":"8820","checksum":"658ba90979ca9528a2efdfac8547047a","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":370,"issue":"6516","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"abstract":[{"text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 370","month":"10"},{"date_updated":"2023-08-22T12:13:48Z","department":[{"_id":"DaAl"}],"_id":"8722","status":"public","conference":{"start_date":"2020-02-22","location":"San Diego, CA, United States","end_date":"2020-02-26","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy.","lang":"eng"}],"month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1908.04207","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528.","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.","ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61.","short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61."},"title":"Taming unbalanced training workloads in deep learning with partial collective operations","article_processing_charge":"No","external_id":{"isi":["000564476500004"],"arxiv":["1908.04207"]},"author":[{"last_name":"Li","full_name":"Li, Shigang","first_name":"Shigang"},{"last_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun","first_name":"Tal Ben-Nun"},{"first_name":"Salvatore Di","full_name":"Girolamo, Salvatore Di","last_name":"Girolamo"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"}],"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"01","year":"2020","isi":1,"date_created":"2020-11-05T15:25:30Z","doi":"10.1145/3332466.3374528","date_published":"2020-02-01T00:00:00Z","page":"45-61","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery"},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","doi":"10.1038/s41467-020-19372-x","date_published":"2020-11-04T00:00:00Z","date_created":"2020-11-09T07:49:36Z","has_accepted_license":"1","isi":1,"year":"2020","day":"04","publication":"Nature Communications","article_number":"5569","author":[{"last_name":"Schulte","full_name":"Schulte, Linda","first_name":"Linda"},{"full_name":"Mao, Jiafei","last_name":"Mao","first_name":"Jiafei"},{"first_name":"Julian","full_name":"Reitz, Julian","last_name":"Reitz"},{"first_name":"Sridhar","full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu"},{"first_name":"Denis","last_name":"Kudlinzki","full_name":"Kudlinzki, Denis"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Meier-Credo","full_name":"Meier-Credo, Jakob","first_name":"Jakob"},{"first_name":"Krishna","full_name":"Saxena, Krishna","last_name":"Saxena"},{"first_name":"Florian","full_name":"Buhr, Florian","last_name":"Buhr"},{"first_name":"Julian D.","full_name":"Langer, Julian D.","last_name":"Langer"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"last_name":"Frangakis","full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S."},{"full_name":"Glaubitz, Clemens","last_name":"Glaubitz","first_name":"Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"article_processing_charge":"No","external_id":{"isi":["000592028600001"]},"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","citation":{"ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"11","intvolume":" 11","abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"oa_version":"Published Version","volume":11,"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"file_name":"2020_NatureComm_Schulte.pdf","date_created":"2020-11-09T07:56:24Z","file_size":1670898,"date_updated":"2020-11-09T07:56:24Z","creator":"dernst","success":1,"file_id":"8745","checksum":"b2688f0347e69e6629bba582077278c5","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"_id":"8744","file_date_updated":"2020-11-09T07:56:24Z","department":[{"_id":"EM-Fac"}],"date_updated":"2023-08-22T12:36:07Z","ddc":["570"]},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"40","volume":8,"ec_funded":1,"oa_version":"None","abstract":[{"text":"Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3.","lang":"eng"}],"month":"10","intvolume":" 8","scopus_import":"1","date_updated":"2023-08-22T12:41:05Z","department":[{"_id":"MaIb"}],"_id":"8747","status":"public","article_type":"original","type":"journal_article","day":"28","publication":"Journal of Materials Chemistry C","isi":1,"year":"2020","date_published":"2020-10-28T00:00:00Z","doi":"10.1039/D0TC02182B","date_created":"2020-11-09T08:37:51Z","page":"14092-14099","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council for scholarship support. M. C. has received funding from the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat \r\nAuto`noma de Barcelona Materials Science PhD program.","publisher":"Royal Society of Chemistry","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol, Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B.","ista":"Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M, Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099.","mla":"Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B.","apa":"Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot, A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/D0TC02182B","ama":"Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 2020;8(40):14092-14099. doi:10.1039/D0TC02182B","ieee":"Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” Journal of Materials Chemistry C, vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020.","short":"Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid, M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099."},"title":"Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks","author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu"},{"first_name":"Mariano","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"first_name":"Congcong","full_name":"Xing, Congcong","last_name":"Xing"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"external_id":{"isi":["000581559100015"]},"article_processing_charge":"No","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"_id":"8767","status":"public","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-08-22T12:49:18Z","file_date_updated":"2020-11-18T07:26:10Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"month":"11","intvolume":" 16","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","file_id":"8768","file_size":2498594,"date_updated":"2020-11-18T07:26:10Z","creator":"dernst","file_name":"2020_PlosCompBio_Kaveh.pdf","date_created":"2020-11-18T07:26:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"publication_status":"published","volume":16,"issue":"11","article_number":"e1008402","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402."},"title":"The Moran process on 2-chromatic graphs","author":[{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"first_name":"Alex","last_name":"McAvoy","full_name":"McAvoy, Alex"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"external_id":{"isi":["000591317200004"]},"article_processing_charge":"No","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"day":"05","publication":"PLOS Computational Biology","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1371/journal.pcbi.1008402","date_published":"2020-11-05T00:00:00Z","date_created":"2020-11-18T07:20:23Z"},{"date_published":"2020-12-04T00:00:00Z","doi":"10.1109/MEMOCODE51338.2020.9314994","date_created":"2020-11-10T07:04:57Z","isi":1,"year":"2020","day":"04","publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","quality_controlled":"1","publisher":"IEEE","oa":1,"author":[{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"first_name":"Daniel","last_name":"Freire","full_name":"Freire, Daniel"},{"last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"external_id":{"arxiv":["2006.12325"],"isi":["000661920400013"]},"article_processing_charge":"No","title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","citation":{"mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994.","apa":"Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994","ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020.","chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994.","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"9314994","ec_funded":1,"publication_identifier":{"isbn":["9781728191485"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.12325"}],"month":"12","abstract":[{"text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"ToHe"}],"date_updated":"2023-08-22T12:48:18Z","type":"conference","conference":{"end_date":"2020-12-04","location":"Virtual Conference","start_date":"2020-12-02","name":"MEMOCODE: Conference on Formal Methods and Models for System Design"},"status":"public","_id":"8750"},{"citation":{"ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303.","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02663-4.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” Journal of Statistical Physics, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","apa":"Maas, J., & Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02663-4","ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 2020;181(6):2257-2303. doi:10.1007/s10955-020-02663-4","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:10.1007/s10955-020-02663-4."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mielke","full_name":"Mielke, Alexander","first_name":"Alexander"}],"external_id":{"arxiv":["2004.02831"],"isi":["000587107200002"]},"article_processing_charge":"No","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Statistical Physics","page":"2257-2303","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s10955-020-02663-4","date_created":"2020-11-15T23:01:18Z","acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-22T13:24:27Z","ddc":["510"],"file_date_updated":"2021-02-04T10:29:11Z","department":[{"_id":"JaMa"}],"_id":"8758","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"bc2b63a90197b97cbc73eccada4639f5","file_id":"9087","success":1,"date_updated":"2021-02-04T10:29:11Z","file_size":753596,"creator":"dernst","date_created":"2021-02-04T10:29:11Z","file_name":"2020_JourStatPhysics_Maas.pdf"}],"language":[{"iso":"eng"}],"volume":181,"issue":"6","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels."}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 181"},{"date_created":"2023-05-23T16:42:30Z","related_material":{"record":[{"relation":"used_in_publication","id":"8755","status":"public"}]},"date_published":"2020-09-27T00:00:00Z","doi":"10.5281/ZENODO.4052882","year":"2020","day":"27","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"publisher":"Zenodo","month":"09","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"},{"first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","full_name":"Trioni, Andrea"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"title":"Surpassing the resistance quantum with a geometric superinductor","department":[{"_id":"JoFi"}],"date_updated":"2023-08-22T13:23:57Z","citation":{"chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13070"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","date_created":"2020-11-22T23:01:23Z","doi":"10.1038/s41467-020-19515-0","date_published":"2020-11-13T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"13","project":[{"grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"article_number":"5778","article_processing_charge":"No","external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"author":[{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"first_name":"Karin","full_name":"Schiefelbein, Karin","last_name":"Schiefelbein"},{"last_name":"Lipsky","full_name":"Lipsky, Silvia","first_name":"Silvia"},{"full_name":"Leunig, Alexander","last_name":"Leunig","first_name":"Alexander"},{"first_name":"Marie","full_name":"Hoffknecht, Marie","last_name":"Hoffknecht"},{"first_name":"Kami","full_name":"Pekayvaz, Kami","last_name":"Pekayvaz"},{"last_name":"Raude","full_name":"Raude, Ben","first_name":"Ben"},{"first_name":"Charlotte","full_name":"Marx, Charlotte","last_name":"Marx"},{"full_name":"Ehrlich, Andreas","last_name":"Ehrlich","first_name":"Andreas"},{"first_name":"Joachim","last_name":"Pircher","full_name":"Pircher, Joachim"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"first_name":"Inas","last_name":"Saleh","full_name":"Saleh, Inas"},{"first_name":"Anna-Kristina","full_name":"Marel, Anna-Kristina","last_name":"Marel"},{"last_name":"Löf","full_name":"Löf, Achim","first_name":"Achim"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"last_name":"Lorenz","full_name":"Lorenz, Michael","first_name":"Michael"},{"last_name":"Stark","full_name":"Stark, Konstantin","first_name":"Konstantin"},{"full_name":"Pick, Robert","last_name":"Pick","first_name":"Robert"},{"full_name":"Rosenberger, Gerhild","last_name":"Rosenberger","first_name":"Gerhild"},{"first_name":"Ludwig","last_name":"Weckbach","full_name":"Weckbach, Ludwig"},{"full_name":"Uhl, Bernd","last_name":"Uhl","first_name":"Bernd"},{"first_name":"Sheng","full_name":"Xia, Sheng","last_name":"Xia"},{"last_name":"Reichel","full_name":"Reichel, Christoph Andreas","first_name":"Christoph Andreas"},{"full_name":"Walzog, Barbara","last_name":"Walzog","first_name":"Barbara"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"first_name":"Markus","full_name":"Bender, Markus","last_name":"Bender"},{"last_name":"Li","full_name":"Li, Rong","first_name":"Rong"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"},{"first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner"}],"title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","citation":{"short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 11","month":"11","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"volume":11,"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"485b7b6cf30198ba0ce126491a28f125","file_id":"8798","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-23T13:29:49Z","file_name":"2020_NatureComm_Nicolai.pdf","date_updated":"2020-11-23T13:29:49Z","file_size":7035340,"creator":"dernst"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8787","file_date_updated":"2020-11-23T13:29:49Z","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"date_updated":"2023-08-22T13:26:26Z","ddc":["570"]},{"_id":"8789","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2023-08-22T13:25:45Z","file_date_updated":"2020-11-23T13:06:30Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.","lang":"eng"}],"intvolume":" 8","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8797","checksum":"61cfcc3b35760656ce7a9385a4ace5d2","success":1,"date_updated":"2020-11-23T13:06:30Z","file_size":565191,"creator":"dernst","date_created":"2020-11-23T13:06:30Z","file_name":"2020_Mathematics_Kleshnina.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["22277390"]},"ec_funded":1,"volume":8,"issue":"11","article_number":"1945","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8111945.","ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics, vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","apa":"Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. Mathematics. 2020;8(11). doi:10.3390/math8111945"},"title":"Prioritised learning in snowdrift-type games","article_processing_charge":"No","external_id":{"isi":["000593962100001"]},"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"},{"first_name":"Sabrina","full_name":"Streipert, Sabrina","last_name":"Streipert"},{"first_name":"Jerzy","last_name":"Filar","full_name":"Filar, Jerzy"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","oa":1,"quality_controlled":"1","publisher":"MDPI","publication":"Mathematics","day":"04","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-11-22T23:01:24Z","doi":"10.3390/math8111945","date_published":"2020-11-04T00:00:00Z"},{"file_date_updated":"2020-08-24T12:53:15Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-22T13:27:32Z","keyword":["reachability","hybrid systems","decomposition"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"EMSOFT: International Conference on Embedded Software","start_date":"2020-09-20","end_date":"2020-09-25","location":"Virtual "},"type":"conference","_id":"8287","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"8790","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"creator":"cschilli","file_size":696384,"date_updated":"2020-08-24T12:53:15Z","file_name":"2020EMSOFT.pdf","date_created":"2020-08-24T12:53:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75","file_id":"8288"}],"publication_status":"published","oa_version":"Preprint","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"}],"title":"Reachability analysis of linear hybrid systems via block decomposition","external_id":{"arxiv":["1905.02458"]},"article_processing_charge":"No","author":[{"first_name":"Sergiy","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","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.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","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.","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 .","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020."},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2020-08-24T12:56:20Z","date_published":"2020-01-01T00:00:00Z","publication":"Proceedings of the International Conference on Embedded Software","year":"2020","has_accepted_license":"1","oa":1,"quality_controlled":"1"},{"department":[{"_id":"KrCh"}],"date_updated":"2023-08-22T13:27:05Z","article_type":"original","type":"journal_article","status":"public","_id":"8788","issue":"11","volume":39,"publication_status":"published","publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 39","month":"11","abstract":[{"text":"We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically.","lang":"eng"}],"oa_version":"None","external_id":{"isi":["000587712700069"]},"article_processing_charge":"No","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Nico","full_name":"Schaumberger, Nico","last_name":"Schaumberger"},{"last_name":"Schmid","full_name":"Schmid, Ulrich","first_name":"Ulrich"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"title":"Precedence-aware automated competitive analysis of real-time scheduling","citation":{"chicago":"Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012803.","ista":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 3981–3992.","mla":"Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:10.1109/TCAD.2020.3012803.","ama":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):3981-3992. doi:10.1109/TCAD.2020.3012803","apa":"Pavlogiannis, A., Schaumberger, N., Schmid, U., & Chatterjee, K. (2020). Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012803","ieee":"A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware automated competitive analysis of real-time scheduling,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 3981–3992, 2020.","short":"A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"3981-3992","date_created":"2020-11-22T23:01:24Z","doi":"10.1109/TCAD.2020.3012803","date_published":"2020-11-01T00:00:00Z","year":"2020","isi":1,"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","day":"01","quality_controlled":"1","publisher":"IEEE","acknowledgement":"This work was supported by the Austrian Science Foundation (FWF) under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented in the International Conference on Embedded Software 2020 and appears as part of the ESWEEK-TCAD special issue. "},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012859","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859."},"title":"Reachability analysis of linear hybrid systems via block decomposition","author":[{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"last_name":"Potomkin","full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"article_processing_charge":"No","external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"01","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","isi":1,"year":"2020","date_published":"2020-11-01T00:00:00Z","doi":"10.1109/TCAD.2020.3012859","date_created":"2020-11-22T23:01:25Z","page":"4018-4029","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","quality_controlled":"1","publisher":"IEEE","oa":1,"date_updated":"2023-08-22T13:27:33Z","department":[{"_id":"ToHe"}],"_id":"8790","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"publication_status":"published","volume":39,"issue":"11","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8287"}]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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 article, 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."}],"month":"11","intvolume":" 39","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.02458"}]},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"8924","file_date_updated":"2020-12-09T09:14:19Z","department":[{"_id":"EvBe"}],"ddc":["580"],"date_updated":"2023-08-24T10:50:00Z","intvolume":" 11","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression.","lang":"eng"}],"volume":11,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_Frontiers_Nibau.pdf","date_created":"2020-12-09T09:14:19Z","creator":"dernst","file_size":1833244,"date_updated":"2020-12-09T09:14:19Z","success":1,"checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","file_id":"8929","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1664-462X"]},"article_number":"586870","title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","article_processing_charge":"No","external_id":{"isi":["000591637000001"]},"author":[{"first_name":"Candida","full_name":"Nibau, Candida","last_name":"Nibau"},{"last_name":"Dadarou","full_name":"Dadarou, Despoina","first_name":"Despoina"},{"full_name":"Kargios, Nestoras","last_name":"Kargios","first_name":"Nestoras"},{"last_name":"Mallioura","full_name":"Mallioura, Areti","first_name":"Areti"},{"full_name":"Fernandez-Fuentes, Narcis","last_name":"Fernandez-Fuentes","first_name":"Narcis"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"first_name":"John H.","full_name":"Doonan, John H.","last_name":"Doonan"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.586870.","ieee":"C. Nibau et al., “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., & Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.586870","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870."},"oa":1,"publisher":"Frontiers","quality_controlled":"1","acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","date_created":"2020-12-06T23:01:14Z","date_published":"2020-11-10T00:00:00Z","doi":"10.3389/fpls.2020.586870","publication":"Frontiers in Plant Science","day":"10","year":"2020","isi":1,"has_accepted_license":"1"},{"publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","page":"13468-13478","date_created":"2020-12-06T23:01:15Z","doi":"10.1021/acscatal.0c03210","date_published":"2020-11-20T00:00:00Z","year":"2020","isi":1,"publication":"ACS Catalysis","day":"20","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"article_processing_charge":"No","external_id":{"isi":["000592978900031"]},"author":[{"last_name":"Irtem","full_name":"Irtem, Erdem","first_name":"Erdem"},{"first_name":"Daniel","full_name":"Arenas Esteban, Daniel","last_name":"Arenas Esteban"},{"last_name":"Duarte","full_name":"Duarte, Miguel","first_name":"Miguel"},{"first_name":"Daniel","full_name":"Choukroun, Daniel","last_name":"Choukroun"},{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"last_name":"Bals","full_name":"Bals, Sara","first_name":"Sara"},{"full_name":"Breugelmans, Tom","last_name":"Breugelmans","first_name":"Tom"}],"title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","citation":{"ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis. American Chemical Society, 2020. https://doi.org/10.1021/acscatal.0c03210.","ieee":"E. Irtem et al., “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” ACS Catalysis, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 2020;10(22):13468-13478. doi:10.1021/acscatal.0c03210","apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.0c03210","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:10.1021/acscatal.0c03210."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 10","month":"11","abstract":[{"text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.","lang":"eng"}],"oa_version":"None","ec_funded":1,"volume":10,"issue":"22","publication_status":"published","publication_identifier":{"eissn":["21555435"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8926","department":[{"_id":"MaIb"}],"date_updated":"2023-08-24T10:52:32Z"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"scopus_import":"1","intvolume":" 102","month":"11","abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.","lang":"eng"}],"oa_version":"Preprint","volume":102,"issue":"18","publication_status":"published","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8944","department":[{"_id":"JoFi"}],"date_updated":"2023-08-24T10:53:36Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","date_created":"2020-12-13T23:01:21Z","doi":"10.1103/PhysRevB.102.180508","date_published":"2020-11-01T00:00:00Z","year":"2020","isi":1,"publication":"Physical Review B","day":"01","article_number":"180508","article_processing_charge":"No","external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]},"author":[{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"last_name":"Szabó","full_name":"Szabó, P.","first_name":"P."},{"first_name":"T.","last_name":"Samuely","full_name":"Samuely, T."},{"full_name":"Kačmarčík, J.","last_name":"Kačmarčík","first_name":"J."},{"last_name":"Neilinger","full_name":"Neilinger, P.","first_name":"P."},{"first_name":"M.","last_name":"Grajcar","full_name":"Grajcar, M."},{"first_name":"P.","last_name":"Samuely","full_name":"Samuely, P."}],"title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","citation":{"mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.","ieee":"M. Zemlicka et al., “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” Physical Review B, vol. 102, no. 18. American Physical Society, 2020.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.102.180508","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 2020;102(18). doi:10.1103/PhysRevB.102.180508","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"8955","file_date_updated":"2020-12-21T10:37:50Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2023-08-24T11:00:45Z","intvolume":" 11","month":"11","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies."}],"ec_funded":1,"volume":11,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"ef9515b28c5619b7126c0f347958bcb3","file_id":"8961","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Frontiers_Rizzo.pdf","date_created":"2020-12-21T10:37:50Z","file_size":13380030,"date_updated":"2020-12-21T10:37:50Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1664042X"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"558070","title":"Network physiology of cortico–muscular interactions","external_id":{"pmid":["33324233"],"isi":["000596849400001"]},"article_processing_charge":"No","author":[{"last_name":"Rizzo","full_name":"Rizzo, Rossella","first_name":"Rossella"},{"first_name":"Xiyun","full_name":"Zhang, Xiyun","last_name":"Zhang"},{"full_name":"Wang, Jilin W.J.L.","last_name":"Wang","first_name":"Jilin W.J.L."},{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"last_name":"Ivanov","full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070."},"oa":1,"quality_controlled":"1","publisher":"Frontiers","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","date_created":"2020-12-20T23:01:18Z","doi":"10.3389/fphys.2020.558070","date_published":"2020-11-26T00:00:00Z","publication":"Frontiers in Physiology","day":"26","year":"2020","has_accepted_license":"1","isi":1},{"isi":1,"has_accepted_license":"1","year":"2020","day":"11","publication":"Cells","date_published":"2020-12-11T00:00:00Z","doi":"10.3390/cells9122662","date_created":"2020-12-14T08:04:03Z","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","publisher":"MDPI","quality_controlled":"1","oa":1,"citation":{"chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells. MDPI, 2020. https://doi.org/10.3390/cells9122662.","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells, vol. 9, no. 12, 2662, MDPI, 2020, doi:10.3390/cells9122662.","ieee":"X. Zhang et al., “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” Cells, vol. 9, no. 12. MDPI, 2020.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 2020;9(12). doi:10.3390/cells9122662","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., & Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. MDPI. https://doi.org/10.3390/cells9122662"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Xuying","last_name":"Zhang","full_name":"Zhang, Xuying"},{"full_name":"Mennicke, Christine V.","last_name":"Mennicke","first_name":"Christine V."},{"last_name":"Xiao","full_name":"Xiao, Guanxi","first_name":"Guanxi"},{"last_name":"Beattie","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Haider, Mansoor","last_name":"Haider","first_name":"Mansoor"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Ghashghaei, H. Troy","last_name":"Ghashghaei","first_name":"H. Troy"}],"external_id":{"isi":["000601787300001"]},"article_processing_charge":"No","title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","article_number":"2662","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"publication_identifier":{"issn":["2073-4409"]},"publication_status":"published","file":[{"checksum":"5095cbdc728c9a510c5761cf60a8861c","file_id":"8950","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-12-14T08:09:43Z","file_name":"2020_Cells_Zhang.pdf","creator":"dernst","date_updated":"2020-12-14T08:09:43Z","file_size":3504525}],"language":[{"iso":"eng"}],"volume":9,"issue":"12","ec_funded":1,"abstract":[{"text":"Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.","lang":"eng"}],"oa_version":"Published Version","month":"12","intvolume":" 9","date_updated":"2023-08-24T10:57:48Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-12-14T08:09:43Z","_id":"8949","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","relation":"press_release","description":"News on IST Homepage"}]},"volume":11,"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-12-28T08:16:10Z","file_size":3958727,"date_created":"2020-12-28T08:16:10Z","file_name":"2020_NatureComm_Faessler.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8975","checksum":"55d43ea0061cc4027ba45e966e1db8cc","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 11","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"file_date_updated":"2020-12-28T08:16:10Z","date_updated":"2023-08-24T11:01:50Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"_id":"8971","date_published":"2020-12-22T00:00:00Z","doi":"10.1038/s41467-020-20286-x","date_created":"2020-12-23T08:25:45Z","has_accepted_license":"1","isi":1,"year":"2020","day":"22","publication":"Nature Communications","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","author":[{"orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Wan, William","last_name":"Wan","first_name":"William"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"external_id":{"isi":["000603078000003"]},"article_processing_charge":"No","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","citation":{"chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"article_number":"6437"},{"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In Progress in Cryptology, 12578:3–15. LNCS. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-65277-7_1.","short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in Progress in Cryptology, Bangalore, India, 2020, vol. 12578, pp. 3–15.","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In Progress in Cryptology (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. https://doi.org/10.1007/978-3-030-65277-7_1","ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: Progress in Cryptology. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:10.1007/978-3-030-65277-7_1","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” Progress in Cryptology, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:10.1007/978-3-030-65277-7_1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000927592800001"]},"author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2020","isi":1,"publication":"Progress in Cryptology","day":"08","page":"3-15","date_created":"2021-01-03T23:01:23Z","doi":"10.1007/978-3-030-65277-7_1","date_published":"2020-12-08T00:00:00Z","series_title":"LNCS","_id":"8987","conference":{"name":"INDOCRYPT: International Conference on Cryptology in India","start_date":"2020-12-13","end_date":"2020-12-16","location":"Bangalore, India"},"type":"conference","status":"public","date_updated":"2023-08-24T11:08:58Z","department":[{"_id":"KrPi"}],"abstract":[{"text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2020/418","open_access":"1"}],"scopus_import":"1","intvolume":" 12578","month":"12","publication_status":"published","publication_identifier":{"issn":["03029743"],"isbn":["9783030652760"],"eissn":["16113349"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":12578},{"department":[{"_id":"CaHe"}],"date_updated":"2023-08-24T11:01:22Z","status":"public","article_type":"original","type":"journal_article","_id":"8957","issue":"6","volume":55,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/relaxing-cell-divisions/"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"publication_status":"published","month":"12","intvolume":" 55","scopus_import":"1","pmid":1,"oa_version":"None","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"abstract":[{"text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation.","lang":"eng"}],"title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","author":[{"last_name":"Godard","full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"full_name":"Dumollard, Rémi","last_name":"Dumollard","first_name":"Rémi"},{"full_name":"Munro, Edwin","last_name":"Munro","first_name":"Edwin"},{"first_name":"Janet","full_name":"Chenevert, Janet","last_name":"Chenevert"},{"last_name":"Hebras","full_name":"Hebras, Céline","first_name":"Céline"},{"first_name":"Alex","last_name":"Mcdougall","full_name":"Mcdougall, Alex"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"pmid":["33207225"],"isi":["000600665700008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016.","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.10.016","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706. doi:10.1016/j.devcel.2020.10.016","ieee":"B. G. Godard et al., “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016.","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706."},"doi":"10.1016/j.devcel.2020.10.016","date_published":"2020-12-21T00:00:00Z","date_created":"2020-12-20T23:01:19Z","page":"695-706","day":"21","publication":"Developmental Cell","isi":1,"year":"2020","quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8)."},{"file":[{"checksum":"69039cd402a571983aa6cb4815ffa863","file_id":"9004","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-01-11T08:37:31Z","file_name":"2020_PNAS_Grah.pdf","date_updated":"2021-01-11T08:37:31Z","file_size":1199247,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/"}]},"volume":117,"issue":"50","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future."}],"month":"12","intvolume":" 117","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-24T11:10:22Z","file_date_updated":"2021-01-11T08:37:31Z","department":[{"_id":"GaTk"}],"_id":"9000","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"15","publication":"PNAS","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-12-15T00:00:00Z","doi":"10.1073/pnas.2006731117","date_created":"2021-01-10T23:01:17Z","page":"31614-31622","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117","short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020."},"title":"Nonequilibrium models of optimal enhancer function","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Benjamin","last_name":"Zoller","full_name":"Zoller, Benjamin"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"article_processing_charge":"No","external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination using a digital receiver,” Science Advances, vol. 6, no. 19. AAAS, 2020.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, Science Advances 6 (2020).","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave quantum illumination using a digital receiver. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abb0451","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination using a digital receiver. Science Advances. 2020;6(19). doi:10.1126/sciadv.abb0451","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination Using a Digital Receiver.” Science Advances, vol. 6, no. 19, eabb0451, AAAS, 2020, doi:10.1126/sciadv.abb0451.","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination using a digital receiver. Science Advances. 6(19), eabb0451.","chicago":"Barzanjeh, Shabir, S. Pirandola, D Vitali, and Johannes M Fink. “Microwave Quantum Illumination Using a Digital Receiver.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abb0451."},"title":"Microwave quantum illumination using a digital receiver","author":[{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pirandola, S.","last_name":"Pirandola","first_name":"S."},{"first_name":"D","full_name":"Vitali, D","last_name":"Vitali"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.03058"],"isi":["000531171100045"]},"article_number":"eabb0451","project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105"}],"day":"06","publication":"Science Advances","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-05-06T00:00:00Z","doi":"10.1126/sciadv.abb0451","date_created":"2020-05-31T22:00:49Z","publisher":"AAAS","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-08-24T11:10:49Z","file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"JoFi"}],"_id":"7910","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"16fa61cc1951b444ee74c07188cda9da","file_id":"7913","creator":"dernst","file_size":795822,"date_updated":"2020-07-14T12:48:05Z","file_name":"2020_ScienceAdvances_Barzanjeh.pdf","date_created":"2020-06-02T09:18:36Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","issue":"19","volume":6,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/scientists-demonstrate-quantum-radar-prototype/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"9001","relation":"later_version"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits."}],"month":"05","intvolume":" 6","scopus_import":"1"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits."}],"month":"09","intvolume":" 2020","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1908.03058","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1097-5659"],"isbn":["9781728189420"]},"publication_status":"published","volume":2020,"related_material":{"record":[{"status":"public","id":"7910","relation":"earlier_version"}]},"issue":"9","ec_funded":1,"_id":"9001","status":"public","type":"conference","conference":{"name":"RadarConf: National Conference on Radar","end_date":"2020-09-25","location":"Florence, Italy","start_date":"2020-09-21"},"date_updated":"2023-08-24T11:10:49Z","department":[{"_id":"JoFi"}],"acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie Skłodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","quality_controlled":"1","publisher":"IEEE","oa":1,"day":"21","publication":"IEEE National Radar Conference - Proceedings","isi":1,"year":"2020","doi":"10.1109/RadarConf2043947.2020.9266397","date_published":"2020-09-21T00:00:00Z","date_created":"2021-01-10T23:01:17Z","article_number":"9266397","project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In IEEE National Radar Conference - Proceedings, Vol. 2020. IEEE, 2020. https://doi.org/10.1109/RadarConf2043947.2020.9266397.","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” IEEE National Radar Conference - Proceedings, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:10.1109/RadarConf2043947.2020.9266397.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in IEEE National Radar Conference - Proceedings, Florence, Italy, 2020, vol. 2020, no. 9.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In IEEE National Radar Conference - Proceedings (Vol. 2020). Florence, Italy: IEEE. https://doi.org/10.1109/RadarConf2043947.2020.9266397","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: IEEE National Radar Conference - Proceedings. Vol 2020. IEEE; 2020. doi:10.1109/RadarConf2043947.2020.9266397"},"title":"Microwave quantum illumination with a digital phase-conjugated receiver","author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh"},{"first_name":"Stefano","full_name":"Pirandola, Stefano","last_name":"Pirandola"},{"first_name":"David","last_name":"Vitali","full_name":"Vitali, David"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.03058"],"isi":["000612224900089"]}},{"_id":"9007","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-24T11:11:36Z","department":[{"_id":"TiBr"}],"oa_version":"Preprint","abstract":[{"text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.","lang":"eng"}],"intvolume":" 95","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1906.08463","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["14208946"],"issn":["00102571"]},"volume":95,"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:10.4171/CMH/499.","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” Commentarii Mathematici Helvetici, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 2020;95(4):635-659. doi:10.4171/CMH/499","apa":"Browning, T. D., & Sawin, W. (2020). Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. European Mathematical Society. https://doi.org/10.4171/CMH/499","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici. European Mathematical Society, 2020. https://doi.org/10.4171/CMH/499.","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659."},"title":"Free rational points on smooth hypersurfaces","external_id":{"isi":["000596833300001"],"arxiv":["1906.08463"]},"article_processing_charge":"No","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sawin","full_name":"Sawin, Will","first_name":"Will"}],"oa":1,"publisher":"European Mathematical Society","quality_controlled":"1","publication":"Commentarii Mathematici Helvetici","day":"07","year":"2020","isi":1,"date_created":"2021-01-17T23:01:11Z","doi":"10.4171/CMH/499","date_published":"2020-12-07T00:00:00Z","page":"635-659"},{"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"article_number":"020315","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","article_processing_charge":"No","external_id":{"isi":["000674680100001"]},"author":[{"orcid":"0000-0001-9868-2166","full_name":"Hease, William J","last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald G.L. Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” PRX Quantum. American Physical Society, 2020. https://doi.org/10.1103/prxquantum.1.020315.","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel HGL, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 1(2), 020315.","mla":"Hease, William J., et al. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” PRX Quantum, vol. 1, no. 2, 020315, American Physical Society, 2020, doi:10.1103/prxquantum.1.020315.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H. G. L., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.1.020315","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 2020;1(2). doi:10.1103/prxquantum.1.020315","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H.G.L. Schwefel, J.M. Fink, PRX Quantum 1 (2020).","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state,” PRX Quantum, vol. 1, no. 2. American Physical Society, 2020."},"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"The authors acknowledge the support of T. Menner, A. Arslani, and T. Asenov from the Miba machine shop for machining the microwave cavity, and thank S. Barzanjeh, F. Sedlmeir, and C. Marquardt for fruitful discussions. This work is supported by IST Austria and the European Research Council under Grant No. 758053 (ERC StG QUNNECT). W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411.\r\nG.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71) and the European Union’s Horizon 2020 research and innovation program under Grant No. 899354 (FET Open SuperQuLAN). H.G.L.S. acknowledges support from the Aotearoa/New Zealand’s MBIE Endeavour Smart Ideas Grant No UOOX1805.","date_created":"2021-02-12T10:41:28Z","date_published":"2020-11-23T00:00:00Z","doi":"10.1103/prxquantum.1.020315","publication":"PRX Quantum","day":"23","year":"2020","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9114","file_date_updated":"2021-02-12T11:16:16Z","department":[{"_id":"JoFi"}],"ddc":["530"],"date_updated":"2023-08-24T11:16:36Z","intvolume":" 1","month":"11","oa_version":"Published Version","abstract":[{"text":"Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion\r\nefficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"13071","relation":"research_data"},{"status":"public","id":"12900","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"13175","status":"public"}]},"issue":"2","volume":1,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":2146924,"date_updated":"2021-02-12T11:16:16Z","file_name":"2020_PRXQuantum_Hease.pdf","date_created":"2021-02-12T11:16:16Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"b70b12ded6d7660d4c9037eb09bfed0c","file_id":"9115"}],"publication_status":"published","publication_identifier":{"issn":["2691-3399"]}},{"issue":"2","volume":5,"ec_funded":1,"file":[{"file_id":"9215","checksum":"a8562c42124a66b86836fe2489eb5f4f","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-03-02T09:47:13Z","file_name":"2020_QuantumScience_Lauk.pdf","date_updated":"2021-03-02T09:47:13Z","file_size":974399,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2058-9565"]},"publication_status":"published","month":"03","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future."}],"department":[{"_id":"JoFi"}],"file_date_updated":"2021-03-02T09:47:13Z","ddc":["530"],"date_updated":"2023-08-24T11:17:48Z","status":"public","article_type":"review","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9194","doi":"10.1088/2058-9565/ab788a","date_published":"2020-03-01T00:00:00Z","date_created":"2021-02-25T08:32:29Z","day":"01","publication":"Quantum Science and Technology","has_accepted_license":"1","isi":1,"year":"2020","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"acknowledgement":"During the writing of this article we became aware of another review of quantum transduction with somewhat different emphasis [99].\r\nWe would like to thank the participants of the transduction workshop at Caltech in September 2018 for helpful and stimulating discussions. We particularly thank John Bartholomew, Andrei Faraon, Johannes Fink, Jeff Holzgrafe, Linbo Shao, Marko Lončar, Daniel Oblak, and Oskar Painter.\r\nN L and N S acknowledge support from the Alliance for Quantum Technologies' (AQT) Intelligent Quantum Networks and Technologies (INQNET) research program and by DOE/HEP QuantISED program grant, QCCFP (Quantum Communication Channels for Fundamental Physics), award number DE-SC0019219. NS further acknowledges support by the Natural Sciences and Engineering Research Council of Canada (NSERC). SB acknowledges support from the Marie Skłodowska Curie fellowship number 707 438 (MSC-IF SUPEREOM). JPC acknowledges support from the Caltech PMA prize postdoctoral fellowship. MS acknowledges support from the ARL-CDQI and the National Science Foundation. CS acknowledges NSERC, Quantum Alberta, and the Alberta Major Innovation Fund.","title":"Perspectives on quantum transduction","author":[{"last_name":"Lauk","full_name":"Lauk, Nikolai","first_name":"Nikolai"},{"full_name":"Sinclair, Neil","last_name":"Sinclair","first_name":"Neil"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Jacob P","full_name":"Covey, Jacob P","last_name":"Covey"},{"last_name":"Saffman","full_name":"Saffman, Mark","first_name":"Mark"},{"full_name":"Spiropulu, Maria","last_name":"Spiropulu","first_name":"Maria"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"external_id":{"isi":["000521449500001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"N. Lauk, N. Sinclair, S. Barzanjeh, J.P. Covey, M. Saffman, M. Spiropulu, C. Simon, Quantum Science and Technology 5 (2020).","ieee":"N. Lauk et al., “Perspectives on quantum transduction,” Quantum Science and Technology, vol. 5, no. 2. IOP Publishing, 2020.","apa":"Lauk, N., Sinclair, N., Barzanjeh, S., Covey, J. P., Saffman, M., Spiropulu, M., & Simon, C. (2020). Perspectives on quantum transduction. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab788a","ama":"Lauk N, Sinclair N, Barzanjeh S, et al. Perspectives on quantum transduction. Quantum Science and Technology. 2020;5(2). doi:10.1088/2058-9565/ab788a","mla":"Lauk, Nikolai, et al. “Perspectives on Quantum Transduction.” Quantum Science and Technology, vol. 5, no. 2, 020501, IOP Publishing, 2020, doi:10.1088/2058-9565/ab788a.","ista":"Lauk N, Sinclair N, Barzanjeh S, Covey JP, Saffman M, Spiropulu M, Simon C. 2020. Perspectives on quantum transduction. Quantum Science and Technology. 5(2), 020501.","chicago":"Lauk, Nikolai, Neil Sinclair, Shabir Barzanjeh, Jacob P Covey, Mark Saffman, Maria Spiropulu, and Christoph Simon. “Perspectives on Quantum Transduction.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab788a."},"project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"article_number":"020501"},{"language":[{"iso":"eng"}],"file":[{"file_id":"9041","checksum":"21aa1cf4c30a86a00cae15a984819b5d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-01-25T07:48:39Z","file_name":"2020_SIAM_Fischer.pdf","creator":"dernst","date_updated":"2021-01-25T07:48:39Z","file_size":310655}],"publication_status":"published","publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"ec_funded":1,"volume":52,"issue":"6","oa_version":"Published Version","abstract":[{"text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems.","lang":"eng"}],"intvolume":" 52","month":"12","scopus_import":"1","ddc":["510"],"date_updated":"2023-08-24T11:15:16Z","file_date_updated":"2021-01-25T07:48:39Z","department":[{"_id":"JuFi"}],"_id":"9039","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"SIAM Journal on Mathematical Analysis","day":"15","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2021-01-24T23:01:09Z","doi":"10.1137/20M1322182","date_published":"2020-12-15T00:00:00Z","page":"6222-6233","acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:10.1137/20M1322182.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” SIAM Journal on Mathematical Analysis, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233.","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 2020;52(6):6222-6233. doi:10.1137/20M1322182","apa":"Fischer, J. L., Laux, T., & Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1322182","chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/20M1322182.","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233."},"title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies","article_processing_charge":"No","external_id":{"isi":["000600695200027"]},"author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"last_name":"Laux","full_name":"Laux, Tim","first_name":"Tim"},{"first_name":"Theresa M.","full_name":"Simon, Theresa M.","last_name":"Simon"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"page":"323-348","date_created":"2021-02-07T23:01:15Z","date_published":"2020-11-01T00:00:00Z","doi":"10.1007/s11854-020-0135-2","year":"2020","isi":1,"publication":"Journal d'Analyse Mathematique","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Supported in part by Hong Kong RGC Grant ECS 26301517.\r\nSupported in part by ERC Advanced Grant RANMAT No. 338804.\r\nSupported in part by the Knut and Alice Wallenberg Foundation and the Swedish Research Council Grant VR-2017-05195.","external_id":{"isi":["000611879400008"],"arxiv":["1804.11199"]},"article_processing_charge":"No","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"title":"On the support of the free additive convolution","citation":{"mla":"Bao, Zhigang, et al. “On the Support of the Free Additive Convolution.” Journal d’Analyse Mathematique, vol. 142, Springer Nature, 2020, pp. 323–48, doi:10.1007/s11854-020-0135-2.","ama":"Bao Z, Erdös L, Schnelli K. On the support of the free additive convolution. Journal d’Analyse Mathematique. 2020;142:323-348. doi:10.1007/s11854-020-0135-2","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2020). On the support of the free additive convolution. Journal d’Analyse Mathematique. Springer Nature. https://doi.org/10.1007/s11854-020-0135-2","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “On the support of the free additive convolution,” Journal d’Analyse Mathematique, vol. 142. Springer Nature, pp. 323–348, 2020.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal d’Analyse Mathematique 142 (2020) 323–348.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “On the Support of the Free Additive Convolution.” Journal d’Analyse Mathematique. Springer Nature, 2020. https://doi.org/10.1007/s11854-020-0135-2.","ista":"Bao Z, Erdös L, Schnelli K. 2020. On the support of the free additive convolution. Journal d’Analyse Mathematique. 142, 323–348."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"volume":142,"publication_status":"published","publication_identifier":{"eissn":["15658538"],"issn":["00217670"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11199"}],"scopus_import":"1","intvolume":" 142","month":"11","abstract":[{"lang":"eng","text":"We consider the free additive convolution of two probability measures μ and ν on the real line and show that μ ⊞ v is supported on a single interval if μ and ν each has single interval support. Moreover, the density of μ ⊞ ν is proven to vanish as a square root near the edges of its support if both μ and ν have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5]."}],"oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_updated":"2023-08-24T11:16:03Z","type":"journal_article","article_type":"original","status":"public","_id":"9104"},{"article_processing_charge":"No","author":[{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sahu","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","department":[{"_id":"JoFi"}],"citation":{"mla":"Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025.","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025."},"date_updated":"2023-08-24T11:16:35Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13071","date_created":"2023-05-23T16:44:11Z","doi":"10.5281/ZENODO.4266025","date_published":"2020-11-10T00:00:00Z","related_material":{"record":[{"status":"public","id":"9114","relation":"used_in_publication"}]},"year":"2020","day":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"oa":1,"publisher":"Zenodo","month":"11","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request."}],"oa_version":"Published Version"},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"9195","department":[{"_id":"JoFi"}],"file_date_updated":"2021-03-02T12:30:03Z","ddc":["530"],"date_updated":"2023-08-24T13:53:02Z","month":"01","intvolume":" 3","oa_version":"Published Version","abstract":[{"text":"Quantum information technology based on solid state qubits has created much interest in converting quantum states from the microwave to the optical domain. Optical photons, unlike microwave photons, can be transmitted by fiber, making them suitable for long distance quantum communication. Moreover, the optical domain offers access to a large set of very well‐developed quantum optical tools, such as highly efficient single‐photon detectors and long‐lived quantum memories. For a high fidelity microwave to optical transducer, efficient conversion at single photon level and low added noise is needed. Currently, the most promising approaches to build such systems are based on second‐order nonlinear phenomena such as optomechanical and electro‐optic interactions. Alternative approaches, although not yet as efficient, include magneto‐optical coupling and schemes based on isolated quantum systems like atoms, ions, or quantum dots. Herein, the necessary theoretical foundations for the most important microwave‐to‐optical conversion experiments are provided, their implementations are described, and the current limitations and future prospects are discussed.","lang":"eng"}],"related_material":{"link":[{"description":"Cover Page","url":"https://doi.org/10.1002/qute.202070011","relation":"poster"}]},"issue":"1","volume":3,"file":[{"file_name":"2020_AdvQuantumTech_Lambert.pdf","date_created":"2021-03-02T12:30:03Z","creator":"dernst","file_size":2410114,"date_updated":"2021-03-02T12:30:03Z","success":1,"file_id":"9216","checksum":"157e95abd6883c3b35b0fa78ae10775e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2511-9044"]},"publication_status":"published","article_number":"1900077","title":"Coherent conversion between microwave and optical photons - An overview of physical implementations","author":[{"first_name":"Nicholas J.","full_name":"Lambert, Nicholas J.","last_name":"Lambert"},{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Schwefel","full_name":"Schwefel, Harald G. L.","first_name":"Harald G. L."}],"external_id":{"isi":["000548088300001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Lambert, N. J., Rueda Sanchez, A. R., Sedlmeir, F., & Schwefel, H. G. L. (2020). Coherent conversion between microwave and optical photons - An overview of physical implementations. Advanced Quantum Technologies. Wiley. https://doi.org/10.1002/qute.201900077","ama":"Lambert NJ, Rueda Sanchez AR, Sedlmeir F, Schwefel HGL. Coherent conversion between microwave and optical photons - An overview of physical implementations. Advanced Quantum Technologies. 2020;3(1). doi:10.1002/qute.201900077","short":"N.J. Lambert, A.R. Rueda Sanchez, F. Sedlmeir, H.G.L. Schwefel, Advanced Quantum Technologies 3 (2020).","ieee":"N. J. Lambert, A. R. Rueda Sanchez, F. Sedlmeir, and H. G. L. Schwefel, “Coherent conversion between microwave and optical photons - An overview of physical implementations,” Advanced Quantum Technologies, vol. 3, no. 1. Wiley, 2020.","mla":"Lambert, Nicholas J., et al. “Coherent Conversion between Microwave and Optical Photons - An Overview of Physical Implementations.” Advanced Quantum Technologies, vol. 3, no. 1, 1900077, Wiley, 2020, doi:10.1002/qute.201900077.","ista":"Lambert NJ, Rueda Sanchez AR, Sedlmeir F, Schwefel HGL. 2020. Coherent conversion between microwave and optical photons - An overview of physical implementations. Advanced Quantum Technologies. 3(1), 1900077.","chicago":"Lambert, Nicholas J., Alfredo R Rueda Sanchez, Florian Sedlmeir, and Harald G. L. Schwefel. “Coherent Conversion between Microwave and Optical Photons - An Overview of Physical Implementations.” Advanced Quantum Technologies. Wiley, 2020. https://doi.org/10.1002/qute.201900077."},"quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The authors thank Amita Deb for useful comments on this manuscript. The authors acknowledge support from the MBIE of New Zealand Endeavour Smart Ideas fund. The reference numbers in Figure 8 were corrected in April 2020, after online publication.","doi":"10.1002/qute.201900077","date_published":"2020-01-01T00:00:00Z","date_created":"2021-02-25T08:52:36Z","day":"01","publication":"Advanced Quantum Technologies","isi":1,"has_accepted_license":"1","year":"2020"},{"scopus_import":"1","main_file_link":[{"url":"https://dl.acm.org/doi/10.14778/3436905.3436917","open_access":"1"}],"month":"12","intvolume":" 14","abstract":[{"text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees.","lang":"eng"}],"oa_version":"Published Version","volume":14,"issue":"4","publication_identifier":{"eissn":["2150-8097"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9011","department":[{"_id":"ElKo"}],"date_updated":"2023-08-24T13:57:13Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-Ramón Troncoso Pastoriza, Frédéric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","page":"586-599","doi":"10.14778/3436905.3436917","date_published":"2020-12-01T00:00:00Z","date_created":"2021-01-17T23:01:13Z","isi":1,"year":"2020","day":"01","publication":"Proceedings of the VLDB Endowment","author":[{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Alp","full_name":"Alp, Enis Ceyhun","first_name":"Enis Ceyhun"},{"full_name":"Gasser, Linus","last_name":"Gasser","first_name":"Linus"},{"last_name":"Jovanovic","full_name":"Jovanovic, Philipp","first_name":"Philipp"},{"full_name":"Syta, Ewa","last_name":"Syta","first_name":"Ewa"},{"full_name":"Ford, Bryan","last_name":"Ford","first_name":"Bryan"}],"article_processing_charge":"No","external_id":{"isi":["000658495400012"]},"title":"CALYPSO: Private data management for decentralized ledgers","citation":{"chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” Proceedings of the VLDB Endowment. Association for Computing Machinery, 2020. https://doi.org/10.14778/3436905.3436917.","ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599.","mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” Proceedings of the VLDB Endowment, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:10.14778/3436905.3436917.","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” Proceedings of the VLDB Endowment, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020.","short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599.","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., & Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. Association for Computing Machinery. https://doi.org/10.14778/3436905.3436917","ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 2020;14(4):586-599. doi:10.14778/3436905.3436917"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publisher":"American Physical Society","quality_controlled":"1","oa":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).","date_published":"2020-08-26T00:00:00Z","doi":"10.1103/physrevb.102.060202","date_created":"2020-08-26T19:27:42Z","day":"26","publication":"Physical Review B","isi":1,"has_accepted_license":"1","year":"2020","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"article_number":"060202(R)","title":"Stability of mobility edges in disordered interacting systems","author":[{"first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"external_id":{"isi":["000562628300001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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.","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R)."},"month":"08","intvolume":" 102","scopus_import":"1","oa_version":"None","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."}],"related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"volume":102,"issue":"6","ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"716442fa7861323fcc80b93718ca009c","file_id":"8309","success":1,"date_updated":"2020-08-26T19:28:55Z","file_size":488825,"creator":"mserbyn","date_created":"2020-08-26T19:28:55Z","file_name":"PhysRevB.102.060202.pdf"},{"success":1,"checksum":"be0abdc8f60fe065ea6dc92e08487122","file_id":"8310","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Supplementary-mbme.pdf","date_created":"2020-08-26T19:29:00Z","creator":"mserbyn","file_size":711405,"date_updated":"2020-08-26T19:29:00Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"8308","file_date_updated":"2020-08-26T19:29:00Z","department":[{"_id":"MaSe"}],"ddc":["530"],"date_updated":"2023-08-24T14:20:21Z"},{"abstract":[{"lang":"eng","text":"We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01597"}],"month":"10","intvolume":" 279","publication_identifier":{"issn":["0022-1236"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":279,"issue":"7","ec_funded":1,"_id":"10862","type":"journal_article","article_type":"original","status":"public","keyword":["Analysis"],"date_updated":"2023-08-24T14:08:42Z","department":[{"_id":"LaEr"}],"acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804.","publisher":"Elsevier","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"15","publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2020.108639","date_published":"2020-10-15T00:00:00Z","date_created":"2022-03-18T10:18:59Z","article_number":"108639","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108639.","ista":"Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.","mla":"Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis, vol. 279, no. 7, 108639, Elsevier, 2020, doi:10.1016/j.jfa.2020.108639.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” Journal of Functional Analysis, vol. 279, no. 7. Elsevier, 2020.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020).","ama":"Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 2020;279(7). doi:10.1016/j.jfa.2020.108639","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108639"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"full_name":"Schnelli, Kevin","last_name":"Schnelli","first_name":"Kevin"}],"external_id":{"arxiv":["1708.01597"],"isi":["000559623200009"]},"article_processing_charge":"No","title":"Spectral rigidity for addition of random matrices at the regular edge"},{"department":[{"_id":"HeEd"}],"date_updated":"2023-08-24T14:19:55Z","article_type":"original","type":"journal_article","keyword":["General Mathematics"],"status":"public","_id":"10867","issue":"3","volume":2020,"publication_status":"published","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.07513"}],"scopus_import":"1","intvolume":" 2020","month":"02","abstract":[{"text":"In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"arxiv":["1702.07513"],"isi":["000522852700002"]},"author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"title":"Waist of balls in hyperbolic and spherical spaces","citation":{"chicago":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices. Oxford University Press, 2020. https://doi.org/10.1093/imrn/rny037.","ista":"Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697.","mla":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:10.1093/imrn/rny037.","ieee":"A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” International Mathematics Research Notices, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020.","short":"A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697.","apa":"Akopyan, A., & Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rny037","ama":"Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020;2020(3):669-697. doi:10.1093/imrn/rny037"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"669-697","date_created":"2022-03-18T11:39:30Z","doi":"10.1093/imrn/rny037","date_published":"2020-02-01T00:00:00Z","year":"2020","isi":1,"publication":"International Mathematics Research Notices","day":"01","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":" Supported by the Russian Foundation for Basic Research grant 18-01-00036."},{"abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"oa":1,"publisher":"Royal Society of London","month":"10","year":"2020","day":"15","date_created":"2021-08-06T11:26:57Z","doi":"10.6084/m9.figshare.7957469.v1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6467"}]},"date_published":"2020-10-15T00:00:00Z","_id":"9799","type":"research_data_reference","status":"public","date_updated":"2023-08-25T10:34:41Z","citation":{"ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1.","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","short":"C. Fraisse, J.J. Welch, (2020).","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes"},{"citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","short":"C. Fraisse, J.J. Welch, (2020).","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1"},"date_updated":"2023-08-25T10:34:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"last_name":"Welch","full_name":"Welch, John J.","first_name":"John J."}],"article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","_id":"9798","type":"research_data_reference","status":"public","year":"2020","day":"15","doi":"10.6084/m9.figshare.7957472.v1","date_published":"2020-10-15T00:00:00Z","related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-06T11:18:15Z","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"oa_version":"Published Version","publisher":"Royal Society of London","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957472.v1"}],"oa":1,"month":"10"},{"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"article_number":"2050006","article_processing_charge":"No","external_id":{"arxiv":["1806.08751"],"isi":["000547464400001"]},"author":[{"last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"title":"Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices","citation":{"mla":"Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices: Theory and Application, vol. 9, no. 3, 2050006, World Scientific Publishing, 2020, doi:10.1142/S2010326320500069.","short":"G. Cipolloni, L. Erdös, Random Matrices: Theory and Application 9 (2020).","ieee":"G. Cipolloni and L. Erdös, “Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices,” Random Matrices: Theory and Application, vol. 9, no. 3. World Scientific Publishing, 2020.","apa":"Cipolloni, G., & Erdös, L. (2020). Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. World Scientific Publishing. https://doi.org/10.1142/S2010326320500069","ama":"Cipolloni G, Erdös L. Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. 2020;9(3). doi:10.1142/S2010326320500069","chicago":"Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices: Theory and Application. World Scientific Publishing, 2020. https://doi.org/10.1142/S2010326320500069.","ista":"Cipolloni G, Erdös L. 2020. Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. 9(3), 2050006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","date_created":"2019-05-26T21:59:14Z","doi":"10.1142/S2010326320500069","date_published":"2020-07-01T00:00:00Z","year":"2020","isi":1,"publication":"Random Matrices: Theory and Application","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"6488","department":[{"_id":"LaEr"}],"date_updated":"2023-08-28T08:38:48Z","main_file_link":[{"url":"https://arxiv.org/abs/1806.08751","open_access":"1"}],"scopus_import":"1","intvolume":" 9","month":"07","abstract":[{"lang":"eng","text":"We prove a central limit theorem for the difference of linear eigenvalue statistics of a sample covariance matrix W˜ and its minor W. We find that the fluctuation of this difference is much smaller than those of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of W˜ and W. Our result identifies the fluctuation of the spatial derivative of the approximate Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar result for Wigner matrices, for sample covariance matrices, the fluctuation may entirely vanish."}],"oa_version":"Preprint","ec_funded":1,"issue":"3","volume":9,"publication_status":"published","publication_identifier":{"issn":["20103263"],"eissn":["20103271"]},"language":[{"iso":"eng"}]},{"oa":1,"publisher":"AIP Publishing","quality_controlled":"1","acknowledgement":"This work was partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No.\r\nJP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (No. SEED-18 16-2). We acknowledge Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","date_created":"2020-11-09T08:05:43Z","doi":"10.1063/5.0025965","date_published":"2020-10-26T00:00:00Z","year":"2020","isi":1,"publication":"Applied Physics Letters","day":"26","article_number":"173101","external_id":{"isi":["000591639700001"]},"article_processing_charge":"No","author":[{"full_name":"Miranti, Retno","last_name":"Miranti","first_name":"Retno"},{"first_name":"Ricky Dwi","last_name":"Septianto","full_name":"Septianto, Ricky Dwi"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"first_name":"Maksym V.","full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko"},{"first_name":"Nobuhiro","last_name":"Matsushita","full_name":"Matsushita, Nobuhiro"},{"first_name":"Yoshihiro","last_name":"Iwasa","full_name":"Iwasa, Yoshihiro"},{"last_name":"Bisri","full_name":"Bisri, Satria Zulkarnaen","first_name":"Satria Zulkarnaen"}],"title":"Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids","citation":{"mla":"Miranti, Retno, et al. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters, vol. 117, no. 17, 173101, AIP Publishing, 2020, doi:10.1063/5.0025965.","ama":"Miranti R, Septianto RD, Ibáñez M, et al. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 2020;117(17). doi:10.1063/5.0025965","apa":"Miranti, R., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., Iwasa, Y., & Bisri, S. Z. (2020). Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0025965","ieee":"R. Miranti et al., “Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids,” Applied Physics Letters, vol. 117, no. 17. AIP Publishing, 2020.","short":"R. Miranti, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, Applied Physics Letters 117 (2020).","chicago":"Miranti, Retno, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters. AIP Publishing, 2020. https://doi.org/10.1063/5.0025965.","ista":"Miranti R, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 117(17), 173101."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://doi.org/10.1063/5.0025965","open_access":"1"}],"scopus_import":"1","intvolume":" 117","month":"10","abstract":[{"text":"Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron \r\n ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. ","lang":"eng"}],"oa_version":"Published Version","issue":"17","volume":117,"publication_status":"published","publication_identifier":{"eissn":["1077-3118"],"issn":["0003-6951"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8746","department":[{"_id":"MaIb"}],"date_updated":"2023-09-05T11:57:23Z"},{"abstract":[{"text":"The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","month":"03","intvolume":" 120","publication_identifier":{"eissn":["1520-6890"],"issn":["0009-2665"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8060","checksum":"1a683353d46c5841c8bb2ee0a56ac7be","file_size":8525678,"date_updated":"2020-07-14T12:48:06Z","creator":"sfreunbe","file_name":"ChemRev_final.pdf","date_created":"2020-06-29T16:36:01Z"}],"language":[{"iso":"eng"}],"issue":"14","volume":120,"_id":"7985","type":"journal_article","article_type":"review","status":"public","date_updated":"2023-09-05T12:04:28Z","ddc":["540"],"file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"StFr"}],"acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 636069).","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"05","publication":"Chemical Reviews","page":"6626-6683","doi":"10.1021/acs.chemrev.9b00609","date_published":"2020-03-05T00:00:00Z","date_created":"2020-06-19T08:42:47Z","citation":{"mla":"Kwak, WJ, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews, vol. 120, no. 14, American Chemical Society, 2020, pp. 6626–83, doi:10.1021/acs.chemrev.9b00609.","short":"W. Kwak, D. Sharon, C. Xia, H. Kim, L. Johnson, P. Bruce, L. Nazar, Y. Sun, A. Frimer, M. Noked, S.A. Freunberger, D. Aurbach, Chemical Reviews 120 (2020) 6626–6683.","ieee":"W. Kwak et al., “Lithium-oxygen batteries and related systems: Potential, status, and future,” Chemical Reviews, vol. 120, no. 14. American Chemical Society, pp. 6626–6683, 2020.","apa":"Kwak, W., Sharon, D., Xia, C., Kim, H., Johnson, L., Bruce, P., … Aurbach, D. (2020). Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.9b00609","ama":"Kwak W, Sharon D, Xia C, et al. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 2020;120(14):6626-6683. doi:10.1021/acs.chemrev.9b00609","chicago":"Kwak, WJ, D Sharon, C Xia, H Kim, LR Johnson, PG Bruce, LF Nazar, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews. American Chemical Society, 2020. https://doi.org/10.1021/acs.chemrev.9b00609.","ista":"Kwak W, Sharon D, Xia C, Kim H, Johnson L, Bruce P, Nazar L, Sun Y, Frimer A, Noked M, Freunberger SA, Aurbach D. 2020. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 120(14), 6626–6683."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Kwak","full_name":"Kwak, WJ","first_name":"WJ"},{"last_name":"Sharon","full_name":"Sharon, D","first_name":"D"},{"first_name":"C","full_name":"Xia, C","last_name":"Xia"},{"full_name":"Kim, H","last_name":"Kim","first_name":"H"},{"last_name":"Johnson","full_name":"Johnson, LR","first_name":"LR"},{"first_name":"PG","last_name":"Bruce","full_name":"Bruce, PG"},{"first_name":"LF","last_name":"Nazar","full_name":"Nazar, LF"},{"first_name":"YK","last_name":"Sun","full_name":"Sun, YK"},{"first_name":"AA","full_name":"Frimer, AA","last_name":"Frimer"},{"first_name":"M","full_name":"Noked, M","last_name":"Noked"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Aurbach","full_name":"Aurbach, D","first_name":"D"}],"article_processing_charge":"No","external_id":{"pmid":["32134255"],"isi":["000555413600008"]},"title":"Lithium-oxygen batteries and related systems: Potential, status, and future"},{"status":"public","type":"journal_article","article_type":"original","_id":"8721","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:02:35Z","month":"10","intvolume":" 370","scopus_import":"1","main_file_link":[{"url":"https://europepmc.org/article/MED/33122378#free-full-text","open_access":"1"}],"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization."}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/molecular-compass-for-cell-orientation/","relation":"press_release","description":"News on IST Homepage"}]},"volume":370,"issue":"6516","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"25239","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","_id":"2699E3D2-B435-11E9-9278-68D0E5697425"}],"title":"Receptor kinase module targets PIN-dependent auxin transport during canalization","author":[{"last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"},{"first_name":"N","full_name":"Rydza, N","last_name":"Rydza"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","first_name":"David","orcid":"0000-0003-2267-106X","full_name":"Domjan, David","last_name":"Domjan"},{"last_name":"Mazur","full_name":"Mazur, E","first_name":"E"},{"first_name":"E","full_name":"Smakowska-Luzan, E","last_name":"Smakowska-Luzan"},{"first_name":"W","last_name":"Smet","full_name":"Smet, W"},{"first_name":"E","full_name":"Mor, E","last_name":"Mor"},{"full_name":"Nolf, J","last_name":"Nolf","first_name":"J"},{"first_name":"B","last_name":"Yang","full_name":"Yang, B"},{"first_name":"W","last_name":"Grunewald","full_name":"Grunewald, W"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","full_name":"Belkhadir, Y","last_name":"Belkhadir"},{"first_name":"B","full_name":"De Rybel, B","last_name":"De Rybel"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"No","external_id":{"isi":["000583031800041"],"pmid":["33122378"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Hajny J, Prat T, Rydza N, et al. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 2020;370(6516):550-557. doi:10.1126/science.aba3178","apa":"Hajny, J., Prat, T., Rydza, N., Rodriguez Solovey, L., Tan, S., Verstraeten, I., … Friml, J. (2020). Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba3178","ieee":"J. Hajny et al., “Receptor kinase module targets PIN-dependent auxin transport during canalization,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, pp. 550–557, 2020.","short":"J. Hajny, T. Prat, N. Rydza, L. Rodriguez Solovey, S. Tan, I. Verstraeten, D. Domjan, E. Mazur, E. Smakowska-Luzan, W. Smet, E. Mor, J. Nolf, B. Yang, W. Grunewald, G. Molnar, Y. Belkhadir, B. De Rybel, J. Friml, Science 370 (2020) 550–557.","mla":"Hajny, Jakub, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science, vol. 370, no. 6516, American Association for the Advancement of Science, 2020, pp. 550–57, doi:10.1126/science.aba3178.","ista":"Hajny J, Prat T, Rydza N, Rodriguez Solovey L, Tan S, Verstraeten I, Domjan D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnar G, Belkhadir Y, De Rybel B, Friml J. 2020. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 370(6516), 550–557.","chicago":"Hajny, Jakub, Tomas Prat, N Rydza, Lesia Rodriguez Solovey, Shutang Tan, Inge Verstraeten, David Domjan, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba3178."},"publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge M. Glanc and Y. Zhang for providing entryclones; Vienna Biocenter Core Facilities (VBCF) for recombinantprotein production and purification; Vienna Biocenter Massspectrometry Facility, Bioimaging, and Life Science Facilities at IST Austria and Proteomics Core Facility CEITEC for a great assistance.Funding:This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 742985) and Austrian Science Fund (FWF): I 3630-B25 to J.F.and by grants from the Austrian Academy of Science through the Gregor Mendel Institute (Y.B.) and the Austrian Agency for International Cooperation in Education and Research (D.D.); the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001) (W.S.); the Research Foundation–Flanders (FWO;Odysseus II G0D0515N) and a European Research Council grant (ERC; StG TORPEDO; 714055) to B.D.R., B.Y., and E.M.; and the Hertha Firnberg Programme postdoctoral fellowship (T-947) from the FWF Austrian Science Fund to E.S.-L.; J.H. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at IST Austria.","date_published":"2020-10-30T00:00:00Z","doi":"10.1126/science.aba3178","date_created":"2020-11-02T10:04:46Z","page":"550-557","day":"30","publication":"Science","isi":1,"year":"2020"},{"citation":{"mla":"Ghazaryan, Areg, et al. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C, vol. 124, no. 21, American Chemical Society, 2020, pp. 11716–21, doi:10.1021/acs.jpcc.0c02584.","apa":"Ghazaryan, A., Paltiel, Y., & Lemeshko, M. (2020). Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.0c02584","ama":"Ghazaryan A, Paltiel Y, Lemeshko M. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 2020;124(21):11716-11721. doi:10.1021/acs.jpcc.0c02584","ieee":"A. Ghazaryan, Y. Paltiel, and M. Lemeshko, “Analytic model of chiral-induced spin selectivity,” The Journal of Physical Chemistry C, vol. 124, no. 21. American Chemical Society, pp. 11716–11721, 2020.","short":"A. Ghazaryan, Y. Paltiel, M. Lemeshko, The Journal of Physical Chemistry C 124 (2020) 11716–11721.","chicago":"Ghazaryan, Areg, Yossi Paltiel, and Mikhail Lemeshko. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C. American Chemical Society, 2020. https://doi.org/10.1021/acs.jpcc.0c02584.","ista":"Ghazaryan A, Paltiel Y, Lemeshko M. 2020. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 124(21), 11716–11721."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000614616200006"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yossi","full_name":"Paltiel, Yossi","last_name":"Paltiel"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"title":"Analytic model of chiral-induced spin selectivity","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"year":"2020","has_accepted_license":"1","isi":1,"publication":"The Journal of Physical Chemistry C","day":"04","page":"11716-11721","date_created":"2020-06-16T14:29:59Z","date_published":"2020-05-04T00:00:00Z","doi":"10.1021/acs.jpcc.0c02584","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","date_updated":"2023-09-05T12:07:15Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-10-20T14:39:47Z","_id":"7968","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["1932-7447"],"eissn":["1932-7455"]},"language":[{"iso":"eng"}],"file":[{"checksum":"25932bb1d0b0a955be0bea4d17facd49","file_id":"8683","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-20T14:39:47Z","file_name":"2020_PhysChemC_Ghazaryan.pdf","creator":"kschuh","date_updated":"2020-10-20T14:39:47Z","file_size":1543429}],"ec_funded":1,"volume":124,"issue":"21","abstract":[{"lang":"eng","text":"Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 124","month":"05"},{"day":"01","publication":"Nano Letters","isi":1,"year":"2020","date_published":"2020-07-01T00:00:00Z","doi":"10.1021/acs.nanolett.0c01673","date_created":"2022-03-18T11:37:38Z","page":"5323-5329","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01673.","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:10.1021/acs.nanolett.0c01673.","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329.","ieee":"J. Duan et al., “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 2020;20(7):5323-5329. doi:10.1021/acs.nanolett.0c01673","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01673"},"title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","author":[{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"first_name":"Nathaniel","last_name":"Capote-Robayna","full_name":"Capote-Robayna, Nathaniel"},{"last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier"},{"first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez"},{"orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y.","last_name":"Nikitin"},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"article_processing_charge":"No","external_id":{"pmid":["32530634"],"isi":["000548893200082"],"arxiv":["2004.14599"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","issue":"7","volume":20,"oa_version":"Preprint","pmid":1,"abstract":[{"text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.","lang":"eng"}],"month":"07","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2004.14599","open_access":"1"}],"date_updated":"2023-09-05T12:05:58Z","department":[{"_id":"NanoFab"}],"_id":"10866","status":"public","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"article_type":"original","type":"journal_article"},{"citation":{"chicago":"Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.045307.","ista":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 102(4), 045307.","mla":"Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B, vol. 102, no. 4, 045307, American Physical Society, 2020, doi:10.1103/physrevb.102.045307.","apa":"Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., & Santos, P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.045307","ama":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 2020;102(4). doi:10.1103/physrevb.102.045307","ieee":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos, “Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids,” Physical Review B, vol. 102, no. 4. American Physical Society, 2020.","short":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000550579100004"],"arxiv":["1910.06015"]},"author":[{"last_name":"Hubert","full_name":"Hubert, C.","first_name":"C."},{"first_name":"K.","last_name":"Cohen","full_name":"Cohen, K."},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"R.","full_name":"Rapaport, R.","last_name":"Rapaport"},{"first_name":"P. V.","last_name":"Santos","full_name":"Santos, P. V."}],"title":"Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids","article_number":"045307","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"year":"2020","isi":1,"publication":"Physical Review B","day":"21","date_created":"2020-09-30T10:33:43Z","date_published":"2020-07-21T00:00:00Z","doi":"10.1103/physrevb.102.045307","acknowledgement":"We thank W. Kaganer for discussions and for comment on the manuscript. We acknowledge the financial support from the German-Israeli Foundation (GIF), grant agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2023-09-05T12:12:10Z","department":[{"_id":"MiLe"}],"_id":"8588","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"4","volume":102,"abstract":[{"lang":"eng","text":"Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)]."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.06015"}],"scopus_import":"1","intvolume":" 102","month":"07"},{"acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2020","isi":1,"publication":"Physical Review B","day":"01","date_created":"2020-11-18T07:34:17Z","doi":"10.1103/physrevb.102.144109","date_published":"2020-10-01T00:00:00Z","article_number":"144109","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"citation":{"ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109.","chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.144109.","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., & Seiringer, R. (2020). Quantum impurity model for anyons. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.144109","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. Physical Review B. 2020;102(14). doi:10.1103/physrevb.102.144109","ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” Physical Review B, vol. 102, no. 14. American Physical Society, 2020.","short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” Physical Review B, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:10.1103/physrevb.102.144109."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000582563300001"],"arxiv":["1912.07890"]},"article_processing_charge":"No","author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lundholm, D.","last_name":"Lundholm","first_name":"D."},{"full_name":"Rougerie, N.","last_name":"Rougerie","first_name":"N."},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"title":"Quantum impurity model for anyons","abstract":[{"lang":"eng","text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1912.07890","open_access":"1"}],"scopus_import":"1","intvolume":" 102","month":"10","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":102,"issue":"14","_id":"8769","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T12:12:30Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}]},{"article_number":"245411","citation":{"chicago":"Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.101.245411.","ista":"Rao P, Serbyn M. 2020. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 101(24), 245411.","mla":"Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B, vol. 101, no. 24, 245411, American Physical Society, 2020, doi:10.1103/physrevb.101.245411.","short":"P. Rao, M. Serbyn, Physical Review B 101 (2020).","ieee":"P. Rao and M. Serbyn, “Gully quantum Hall ferromagnetism in biased trilayer graphene,” Physical Review B, vol. 101, no. 24. American Physical Society, 2020.","ama":"Rao P, Serbyn M. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 2020;101(24). doi:10.1103/physrevb.101.245411","apa":"Rao, P., & Serbyn, M. (2020). Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.101.245411"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","first_name":"Peng","orcid":"0000-0003-1250-0021","full_name":"Rao, Peng","last_name":"Rao"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000538715500010"]},"article_processing_charge":"No","title":"Gully quantum Hall ferromagnetism in biased trilayer graphene","quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2020","day":"15","publication":"Physical Review B","doi":"10.1103/physrevb.101.245411","date_published":"2020-06-15T00:00:00Z","date_created":"2020-06-17T14:52:06Z","_id":"7971","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T12:11:37Z","department":[{"_id":"MaSe"}],"abstract":[{"lang":"eng","text":"Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.05739"}],"month":"06","intvolume":" 101","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":101,"issue":"24"},{"ec_funded":1,"volume":125,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"intvolume":" 125","month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02367"}],"oa_version":"Preprint","abstract":[{"text":"In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.","lang":"eng"}],"department":[{"_id":"BjHo"}],"date_updated":"2023-09-05T12:08:29Z","keyword":["General Physics and Astronomy"],"status":"public","article_type":"original","type":"journal_article","_id":"8634","date_created":"2020-10-08T17:27:32Z","date_published":"2020-08-05T00:00:00Z","doi":"10.1103/physrevlett.125.064501","publication":"Physical Review Letters","day":"05","year":"2020","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"M. F. S. and R. O. G. acknowledge funding from the National Science Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA Grant Agreement No. 291734.","title":"Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits","article_processing_charge":"No","external_id":{"arxiv":["2008.02367"],"isi":["000555785600005"]},"author":[{"full_name":"Suri, Balachandra","last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kageorge, Logan","last_name":"Kageorge","first_name":"Logan"},{"full_name":"Grigoriev, Roman O.","last_name":"Grigoriev","first_name":"Roman O."},{"first_name":"Michael F.","full_name":"Schatz, Michael F.","last_name":"Schatz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Suri, B., Kageorge, L., Grigoriev, R. O., & Schatz, M. F. (2020). Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.064501","ama":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 2020;125(6). doi:10.1103/physrevlett.125.064501","short":"B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020).","ieee":"B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits,” Physical Review Letters, vol. 125, no. 6. American Physical Society, 2020.","mla":"Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters, vol. 125, no. 6, 064501, American Physical Society, 2020, doi:10.1103/physrevlett.125.064501.","ista":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 125(6), 064501.","chicago":"Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.064501."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"064501"},{"article_processing_charge":"No","external_id":{"isi":["000561114000001"],"pmid":["32404488"]},"author":[{"full_name":"Smith, S","last_name":"Smith","first_name":"S"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"first_name":"L","last_name":"Joos","full_name":"Joos, L"},{"first_name":"I","last_name":"Roberts","full_name":"Roberts, I"},{"last_name":"Nikonorova","full_name":"Nikonorova, N","first_name":"N"},{"last_name":"Vu","full_name":"Vu, LD","first_name":"LD"},{"last_name":"Stes","full_name":"Stes, E","first_name":"E"},{"full_name":"Cho, H","last_name":"Cho","first_name":"H"},{"first_name":"A","last_name":"Larrieu","full_name":"Larrieu, A"},{"first_name":"W","full_name":"Xuan, W","last_name":"Xuan"},{"last_name":"Goodall","full_name":"Goodall, B","first_name":"B"},{"first_name":"B","full_name":"van de Cotte, B","last_name":"van de Cotte"},{"first_name":"JM","last_name":"Waite","full_name":"Waite, JM"},{"first_name":"A","full_name":"Rigal, A","last_name":"Rigal"},{"last_name":"R Harborough","full_name":"R Harborough, SR","first_name":"SR"},{"first_name":"G","last_name":"Persiau","full_name":"Persiau, G"},{"last_name":"Vanneste","full_name":"Vanneste, S","first_name":"S"},{"first_name":"GK","last_name":"Kirschner","full_name":"Kirschner, GK"},{"first_name":"E","last_name":"Vandermarliere","full_name":"Vandermarliere, E"},{"last_name":"Martens","full_name":"Martens, L","first_name":"L"},{"full_name":"Stahl, Y","last_name":"Stahl","first_name":"Y"},{"last_name":"Audenaert","full_name":"Audenaert, D","first_name":"D"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Felix, G","last_name":"Felix","first_name":"G"},{"first_name":"R","full_name":"Simon, R","last_name":"Simon"},{"first_name":"M","last_name":"Bennett","full_name":"Bennett, M"},{"first_name":"A","full_name":"Bishopp, A","last_name":"Bishopp"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"last_name":"Ljung","full_name":"Ljung, K","first_name":"K"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"},{"first_name":"S","full_name":"Robert, S","last_name":"Robert"},{"first_name":"J","full_name":"Nemhauser, J","last_name":"Nemhauser"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"first_name":"K","last_name":"Gevaert","full_name":"Gevaert, K"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"first_name":"I","full_name":"De Smet, I","last_name":"De Smet"}],"title":"The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis","citation":{"short":"S. Smith, S. Zhu, L. Joos, I. Roberts, N. Nikonorova, L. Vu, E. Stes, H. Cho, A. Larrieu, W. Xuan, B. Goodall, B. van de Cotte, J. Waite, A. Rigal, S. R Harborough, G. Persiau, S. Vanneste, G. Kirschner, E. Vandermarliere, L. Martens, Y. Stahl, D. Audenaert, J. Friml, G. Felix, R. Simon, M. Bennett, A. Bishopp, G. De Jaeger, K. Ljung, S. Kepinski, S. Robert, J. Nemhauser, I. Hwang, K. Gevaert, T. Beeckman, I. De Smet, Molecular & Cellular Proteomics 19 (2020) 1248–1262.","ieee":"S. Smith et al., “The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis,” Molecular & Cellular Proteomics, vol. 19, no. 8. American Society for Biochemistry and Molecular Biology, pp. 1248–1262, 2020.","apa":"Smith, S., Zhu, S., Joos, L., Roberts, I., Nikonorova, N., Vu, L., … De Smet, I. (2020). The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/mcp.ra119.001826","ama":"Smith S, Zhu S, Joos L, et al. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 2020;19(8):1248-1262. doi:10.1074/mcp.ra119.001826","mla":"Smith, S., et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics, vol. 19, no. 8, American Society for Biochemistry and Molecular Biology, 2020, pp. 1248–62, doi:10.1074/mcp.ra119.001826.","ista":"Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu L, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite J, Rigal A, R Harborough S, Persiau G, Vanneste S, Kirschner G, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett M, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. 2020. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 19(8), 1248–1262.","chicago":"Smith, S, S Zhu, L Joos, I Roberts, N Nikonorova, LD Vu, E Stes, et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology, 2020. https://doi.org/10.1074/mcp.ra119.001826."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Society for Biochemistry and Molecular Biology","quality_controlled":"1","acknowledgement":"We thank Maria Njo, Sarah De Cokere, Marieke Mispelaere and Darren Wells, for practical assistance, Daniël Van Damme for assistance with image analysis, Marnik Vuylsteke for advice on statistics, Catherine Perrot-Rechenmann for useful discussions, Steffen Lau for critical reading oft he manuscript, and Philip Benfey, Gerd Jürgens, Philippe Nacry, Frederik Börnke, and Frans Tax for sharing materials.","page":"1248-1262","date_created":"2020-06-08T10:10:53Z","date_published":"2020-08-01T00:00:00Z","doi":"10.1074/mcp.ra119.001826","year":"2020","has_accepted_license":"1","isi":1,"publication":"Molecular & Cellular Proteomics","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7949","department":[{"_id":"JiFr"}],"file_date_updated":"2021-05-05T10:10:14Z","date_updated":"2023-09-05T12:17:46Z","ddc":["580"],"scopus_import":"1","intvolume":" 19","month":"08","abstract":[{"text":"Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"8","volume":19,"publication_status":"published","publication_identifier":{"eissn":["1535-9484"]},"language":[{"iso":"eng"}],"file":[{"creator":"kschuh","file_size":1632311,"date_updated":"2021-05-05T10:10:14Z","file_name":"2020_MCP_Smith.pdf","date_created":"2021-05-05T10:10:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9373","checksum":"3f3f37b4a1ba2cfd270fc7733dd89680"}]},{"citation":{"mla":"Zhang, Xixi, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell, vol. 32, no. 5, American Society of Plant Biologists, 2020, pp. 1644–64, doi:10.1105/tpc.19.00869.","short":"X. Zhang, M. Adamowski, P. Marhavá, S. Tan, Y. Zhang, L. Rodriguez Solovey, M. Zwiewka, V. Pukyšová, A.S. Sánchez, V.K. Raxwal, C.S. Hardtke, T. Nodzynski, J. Friml, The Plant Cell 32 (2020) 1644–1664.","ieee":"X. Zhang et al., “Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters,” The Plant Cell, vol. 32, no. 5. American Society of Plant Biologists, pp. 1644–1664, 2020.","apa":"Zhang, X., Adamowski, M., Marhavá, P., Tan, S., Zhang, Y., Rodriguez Solovey, L., … Friml, J. (2020). Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.19.00869","ama":"Zhang X, Adamowski M, Marhavá P, et al. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 2020;32(5):1644-1664. doi:10.1105/tpc.19.00869","chicago":"Zhang, Xixi, Maciek Adamowski, Petra Marhavá, Shutang Tan, Yuzhou Zhang, Lesia Rodriguez Solovey, Marta Zwiewka, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.19.00869.","ista":"Zhang X, Adamowski M, Marhavá P, Tan S, Zhang Y, Rodriguez Solovey L, Zwiewka M, Pukyšová V, Sánchez AS, Raxwal VK, Hardtke CS, Nodzynski T, Friml J. 2020. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 32(5), 1644–1664."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000545741500030"],"pmid":["32193204"]},"article_processing_charge":"No","author":[{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan"},{"last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Vendula","last_name":"Pukyšová","full_name":"Pukyšová, Vendula"},{"last_name":"Sánchez","full_name":"Sánchez, Adrià Sans","first_name":"Adrià Sans"},{"full_name":"Raxwal, Vivek Kumar","last_name":"Raxwal","first_name":"Vivek Kumar"},{"first_name":"Christian S.","full_name":"Hardtke, Christian S.","last_name":"Hardtke"},{"first_name":"Tomasz","last_name":"Nodzynski","full_name":"Nodzynski, Tomasz"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"year":"2020","isi":1,"publication":"The Plant Cell","day":"01","page":"1644-1664","date_created":"2020-03-28T07:39:22Z","doi":"10.1105/tpc.19.00869","date_published":"2020-05-01T00:00:00Z","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","date_updated":"2023-09-05T12:21:06Z","department":[{"_id":"JiFr"}],"_id":"7619","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"5","volume":32,"abstract":[{"lang":"eng","text":"Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development."}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.19.00869"}],"scopus_import":"1","intvolume":" 32","month":"05"},{"department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:21:32Z","status":"public","type":"journal_article","article_type":"original","_id":"8607","volume":32,"issue":"11","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"publication_status":"published","month":"11","intvolume":" 32","scopus_import":"1","main_file_link":[{"url":"https://europepmc.org/article/MED/32958564","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants."}],"title":"Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif","author":[{"last_name":"Liu","full_name":"Liu, D","first_name":"D"},{"first_name":"R","full_name":"Kumar, R","last_name":"Kumar"},{"first_name":"Claus","full_name":"LAN, Claus","last_name":"LAN"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"},{"full_name":"Siao, W","last_name":"Siao","first_name":"W"},{"full_name":"Vanhoutte, I","last_name":"Vanhoutte","first_name":"I"},{"full_name":"Wang, P","last_name":"Wang","first_name":"P"},{"first_name":"KW","last_name":"Bender","full_name":"Bender, KW"},{"last_name":"Yperman","full_name":"Yperman, K","first_name":"K"},{"full_name":"Martins, S","last_name":"Martins","first_name":"S"},{"first_name":"X","last_name":"Zhao","full_name":"Zhao, X"},{"full_name":"Vert, G","last_name":"Vert","first_name":"G"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Russinova","full_name":"Russinova, E","first_name":"E"}],"external_id":{"isi":["000600226800021"],"pmid":["32958564"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"D. Liu et al., “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif,” Plant Cell, vol. 32, no. 11. American Society of Plant Biologists, pp. 3598–3612, 2020.","short":"D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K. Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova, Plant Cell 32 (2020) 3598–3612.","apa":"Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova, E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.20.00384","ama":"Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 2020;32(11):3598-3612. doi:10.1105/tpc.20.00384","mla":"Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell, vol. 32, no. 11, American Society of Plant Biologists, 2020, pp. 3598–612, doi:10.1105/tpc.20.00384.","ista":"Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K, Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 32(11), 3598–3612.","chicago":"Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.20.00384."},"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1105/tpc.20.00384","date_published":"2020-11-01T00:00:00Z","date_created":"2020-10-05T12:45:16Z","page":"3598-3612","day":"01","publication":"Plant Cell","isi":1,"year":"2020","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","publication":"Plant Physiology","day":"01","year":"2020","isi":1,"date_created":"2020-04-29T15:23:00Z","date_published":"2020-07-01T00:00:00Z","doi":"10.1104/pp.20.00178","page":"986-997","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00178","ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 2020;183(3):986-997. doi:10.1104/pp.20.00178","ieee":"J. Wang et al., “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” Plant Physiology, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020.","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:10.1104/pp.20.00178.","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997.","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00178."},"title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","article_processing_charge":"No","external_id":{"isi":["000550682000018"],"pmid":["32321842"]},"author":[{"last_name":"Wang","full_name":"Wang, J","first_name":"J"},{"first_name":"E","full_name":"Mylle, E","last_name":"Mylle"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Besbrugge, N","last_name":"Besbrugge","first_name":"N"},{"last_name":"De Jaeger","full_name":"De Jaeger, G","first_name":"G"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"R","full_name":"Pleskot, R","last_name":"Pleskot"},{"full_name":"van Damme, D","last_name":"van Damme","first_name":"D"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex."}],"intvolume":" 183","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.13.948109"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"issue":"3","volume":183,"_id":"7695","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-05T12:20:02Z","department":[{"_id":"JiFr"}]},{"title":"All-pay bidding games on graphs","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1911.08360"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Avni, Guy, Rasmus Ibsen-Jensen, and Josef Tkadlec. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i02.5546.","ista":"Avni G, Ibsen-Jensen R, Tkadlec J. 2020. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 34(02), 1798–1805.","mla":"Avni, Guy, et al. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02, Association for the Advancement of Artificial Intelligence, 2020, pp. 1798–805, doi:10.1609/aaai.v34i02.5546.","ama":"Avni G, Ibsen-Jensen R, Tkadlec J. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 2020;34(02):1798-1805. doi:10.1609/aaai.v34i02.5546","apa":"Avni, G., Ibsen-Jensen, R., & Tkadlec, J. (2020). All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i02.5546","ieee":"G. Avni, R. Ibsen-Jensen, and J. Tkadlec, “All-pay bidding games on graphs,” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02. Association for the Advancement of Artificial Intelligence, pp. 1798–1805, 2020.","short":"G. Avni, R. Ibsen-Jensen, J. Tkadlec, Proceedings of the AAAI Conference on Artificial Intelligence 34 (2020) 1798–1805."},"project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"doi":"10.1609/aaai.v34i02.5546","date_published":"2020-04-03T00:00:00Z","date_created":"2021-02-25T09:05:18Z","page":"1798-1805","day":"03","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","year":"2020","publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","acknowledgement":"This research was supported by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2023-09-05T12:40:00Z","status":"public","type":"journal_article","article_type":"original","conference":{"location":"New York, NY, United States","end_date":"2020-02-12","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"_id":"9197","volume":34,"issue":"02","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"],"issn":["2159-5399"]},"publication_status":"published","month":"04","intvolume":" 34","scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper we introduce and study all-pay bidding games, a class of two player, zero-sum games on graphs. The game proceeds as follows. We place a token on some vertex in the graph and assign budgets to the two players. Each turn, each player submits a sealed legal bid (non-negative and below their remaining budget), which is deducted from their budget and the highest bidder moves the token onto an adjacent vertex. The game ends once a sink is reached, and Player 1 pays Player 2 the outcome that is associated with the sink. The players attempt to maximize their expected outcome. Our games model settings where effort (of no inherent value) needs to be invested in an ongoing and stateful manner. On the negative side, we show that even in simple games on DAGs, optimal strategies may require a distribution over bids with infinite support. A central quantity in bidding games is the ratio of the players budgets. On the positive side, we show a simple FPTAS for DAGs, that, for each budget ratio, outputs an approximation for the optimal strategy for that ratio. We also implement it, show that it performs well, and suggests interesting properties of these games. Then, given an outcome c, we show an algorithm for finding the necessary and sufficient initial ratio for guaranteeing outcome c with probability 1 and a strategy ensuring such. Finally, while the general case has not previously been studied, solving the specific game in which Player 1 wins iff he wins the first two auctions, has been long stated as an open question, which we solve."}]}]