[{"month":"07","publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]},"doi":"10.1109/TSP.2020.3010355","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"external_id":{"arxiv":["1802.04907"],"isi":["000562044500001"]},"isi":1,"quality_controlled":"1","author":[{"last_name":"Gurel","first_name":"Nezihe Merve","full_name":"Gurel, Nezihe Merve"},{"first_name":"Kaan","last_name":"Kara","full_name":"Kara, Kaan"},{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"full_name":"Smith, Tyler","first_name":"Tyler","last_name":"Smith"},{"first_name":"Thomas","last_name":"Lemmin","full_name":"Lemmin, Thomas"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Puschel","first_name":"Markus","full_name":"Puschel, Markus"},{"full_name":"Zhang, Ce","last_name":"Zhang","first_name":"Ce"}],"date_created":"2020-08-16T22:00:56Z","date_updated":"2023-08-22T08:40:08Z","volume":68,"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.","year":"2020","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"IEEE","day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-20T00:00:00Z","publication":"IEEE Transactions on Signal Processing","citation":{"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","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.","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","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.","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.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355."},"article_type":"original","page":"4268-4282","abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"type":"journal_article","oa_version":"Preprint","_id":"8268","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","intvolume":" 68"},{"oa_version":"None","_id":"8271","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13","title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","status":"public","issue":"9","type":"journal_article","date_published":"2020-09-07T00:00:00Z","citation":{"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","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.","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","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.","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.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 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."},"publication":"Molecular Plant","page":"1238-1240","article_type":"original","article_processing_charge":"No","day":"07","scopus_import":"1","author":[{"last_name":"He","first_name":"Peng","full_name":"He, Peng"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Yuzhou"},{"full_name":"Xiao, Guanghui","first_name":"Guanghui","last_name":"Xiao"}],"volume":13,"date_updated":"2023-08-22T08:40:35Z","date_created":"2020-08-16T22:00:57Z","pmid":1,"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.","year":"2020","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","doi":"10.1016/j.molp.2020.07.006","language":[{"iso":"eng"}],"external_id":{"pmid":["32688032"],"isi":["000566895400007"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"month":"09"},{"publication":"Physical Review Materials","citation":{"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","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.","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","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.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","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.","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."},"article_type":"original","date_published":"2020-08-17T00:00:00Z","scopus_import":"1","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"day":"17","article_processing_charge":"Yes","has_accepted_license":"1","_id":"8101","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"title":"Quantitatively consistent scale-spanning model for same-material tribocharging","status":"public","intvolume":" 4","oa_version":"Published Version","file":[{"date_created":"2020-08-17T15:54:20Z","date_updated":"2020-08-17T15:54:20Z","success":1,"checksum":"288fef1eeb6540c6344bb8f7c8159dc9","file_id":"8277","relation":"main_file","creator":"ggrosjea","content_type":"application/pdf","file_size":853753,"file_name":"Grosjean2020.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"8","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2006.07120"],"isi":["000561897000001"]},"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevMaterials.4.082602","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2475-9953"]},"year":"2020","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.","publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","author":[{"first_name":"Galien M","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M"},{"first_name":"Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian"},{"full_name":"Sobarzo Ponce, Juan Carlos A","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"12697"}]},"date_created":"2020-07-07T11:33:54Z","date_updated":"2023-08-22T08:41:32Z","volume":4,"article_number":"082602","file_date_updated":"2020-08-17T15:54:20Z","ec_funded":1},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8325","status":"public","title":"Sandpile solitons via smoothing of superharmonic functions","intvolume":" 378","abstract":[{"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. ","lang":"eng"}],"issue":"9","type":"journal_article","date_published":"2020-09-01T00:00:00Z","publication":"Communications in Mathematical Physics","citation":{"apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","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","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.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 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."},"article_type":"original","page":"1649-1675","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"}],"date_created":"2020-08-30T22:01:13Z","date_updated":"2023-08-22T09:00:03Z","volume":378,"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.","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"ec_funded":1,"doi":"10.1007/s00220-020-03828-8","language":[{"iso":"eng"}],"external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1711.04285","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"09","publication_identifier":{"issn":["00103616"],"eissn":["14320916"]}},{"day":"18","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-08-18T00:00:00Z","publication":"Nature Communications","citation":{"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.","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.","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","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.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","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."},"article_type":"original","abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_size":7527373,"content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","checksum":"52b96f41d7d0db9728064c08da00d030","success":1,"date_updated":"2020-08-31T13:40:00Z","date_created":"2020-08-31T13:40:00Z","relation":"main_file","file_id":"8326"}],"_id":"8318","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Key role of quinone in the mechanism of respiratory complex I","ddc":["570"],"status":"public","intvolume":" 11","month":"08","publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-020-17957-0","language":[{"iso":"eng"}],"external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-08-31T13:40:00Z","article_number":"4135","author":[{"first_name":"Javier","last_name":"Gutierrez-Fernandez","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","full_name":"Gutierrez-Fernandez, Javier"},{"id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","last_name":"Kaszuba","first_name":"Karol","full_name":"Kaszuba, Karol"},{"full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S.","last_name":"Minhas"},{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh"},{"full_name":"Tambalo, Margherita","first_name":"Margherita","last_name":"Tambalo","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a"},{"last_name":"Gallagher","first_name":"David T.","full_name":"Gallagher, David T."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}]},"date_created":"2020-08-30T22:01:10Z","date_updated":"2023-08-22T09:03:00Z","volume":11,"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.","year":"2020","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LeSa"}]},{"oa_version":"None","intvolume":" 54","status":"public","title":"Expanding the genetic code: Unnatural base pairs in biological systems","_id":"8320","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"type":"journal_article","date_published":"2020-08-19T00:00:00Z","page":"475-484","article_type":"original","citation":{"mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","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.","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","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.","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","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."},"publication":"Molecular Biology","article_processing_charge":"No","day":"19","scopus_import":"1","volume":54,"date_updated":"2023-08-22T09:01:03Z","date_created":"2020-08-30T22:01:11Z","related_material":{"record":[{"relation":"original","status":"public","id":"8321"}]},"author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Vlasov","full_name":"Vlasov, Petr"},{"full_name":"Kolosov, P. M.","first_name":"P. M.","last_name":"Kolosov"},{"full_name":"Shuvalova, E. Y.","last_name":"Shuvalova","first_name":"E. Y."},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","year":"2020","language":[{"iso":"eng"}],"doi":"10.1134/S0026893320040111","quality_controlled":"1","isi":1,"external_id":{"isi":["000562110300001"]},"publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"month":"08"},{"publication_identifier":{"issn":["00268984"]},"month":"07","quality_controlled":"1","external_id":{"pmid":["32799218"]},"language":[{"iso":"rus"}],"doi":"10.31857/S0026898420040126","department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","publication_status":"published","pmid":1,"year":"2020","volume":54,"date_updated":"2023-08-22T09:01:02Z","date_created":"2020-08-30T22:01:11Z","related_material":{"record":[{"id":"8320","status":"public","relation":"translation"}]},"author":[{"full_name":"Mukba, S. A.","first_name":"S. A.","last_name":"Mukba"},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr","full_name":"Vlasov, Petr"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"full_name":"Shuvalova, E. Y.","last_name":"Shuvalova","first_name":"E. Y."},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"531-541","article_type":"original","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.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. 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.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126"},"publication":"Molekuliarnaia biologiia","date_published":"2020-07-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"intvolume":" 54","title":"Expanding the genetic code: Unnatural base pairs in biological systems","status":"public","_id":"8321","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"None"},{"doi":"10.1007/s00454-020-00237-5","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00237-5"}],"oa":1,"external_id":{"isi":["000561483500001"]},"isi":1,"month":"10","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"author":[{"full_name":"Pach, János","last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"date_created":"2020-08-30T22:01:12Z","date_updated":"2023-08-22T09:05:04Z","volume":64,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"date_published":"2020-10-01T00:00:00Z","publication":"Discrete and Computational Geometry","citation":{"short":"J. Pach, Discrete and Computational Geometry 64 (2020) 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.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. 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.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. 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."},"article_type":"letter_note","page":"571-574","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8323","status":"public","title":"A farewell to Ricky Pollack","intvolume":" 64","type":"journal_article"},{"department":[{"_id":"EvBe"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2020","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.).","volume":11,"date_created":"2020-09-06T22:01:12Z","date_updated":"2023-08-22T09:09:06Z","author":[{"full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","last_name":"Kubiasova","first_name":"Karolina"},{"orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C","full_name":"Montesinos López, Juan C"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"full_name":"Nisler, Jaroslav","first_name":"Jaroslav","last_name":"Nisler"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana"},{"full_name":"Plíhalová, Lucie","first_name":"Lucie","last_name":"Plíhalová"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Marhavý, Peter","first_name":"Peter","last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"last_name":"Doležal","first_name":"Karel","full_name":"Doležal, Karel"},{"last_name":"Galuszka","first_name":"Petr","full_name":"Galuszka, Petr"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"last_name":"Spíchal","first_name":"Lukáš","full_name":"Spíchal, Lukáš"}],"article_number":"4285","ec_funded":1,"file_date_updated":"2020-09-10T08:05:19Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1038/s41467-020-17949-0","publication_identifier":{"eissn":["20411723"]},"month":"08","intvolume":" 11","ddc":["580"],"status":"public","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8336","file":[{"date_updated":"2020-09-10T08:05:19Z","date_created":"2020-09-10T08:05:19Z","success":1,"checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","file_id":"8357","relation":"main_file","creator":"dernst","file_size":3455704,"content_type":"application/pdf","file_name":"2020_NatureComm_Kubiasova.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"article_type":"original","citation":{"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.","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","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.","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.","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."},"publication":"Nature Communications","date_published":"2020-08-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27"},{"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."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-12-10T12:23:56Z","date_created":"2020-12-10T12:23:56Z","checksum":"5b96f39b598de7510cfefefb819b9a6d","success":1,"relation":"main_file","file_id":"8936","content_type":"application/pdf","file_size":3526415,"creator":"dernst","file_name":"2020_NatureComm_Antoniadi.pdf","access_level":"open_access"}],"title":"Cell-surface receptors enable perception of extracellular cytokinins","status":"public","ddc":["580"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8337","day":"27","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-08-27T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"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.","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.","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).","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.","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"},"file_date_updated":"2020-12-10T12:23:56Z","ec_funded":1,"article_number":"4284","date_created":"2020-09-06T22:01:13Z","date_updated":"2023-08-22T09:10:32Z","volume":11,"author":[{"full_name":"Antoniadi, Ioanna","last_name":"Antoniadi","first_name":"Ioanna"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"first_name":"Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"last_name":"Simerský","first_name":"Radim","full_name":"Simerský, Radim"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"full_name":"Vain, Thomas","last_name":"Vain","first_name":"Thomas"},{"first_name":"Eduardo","last_name":"Mateo-Bonmatí","full_name":"Mateo-Bonmatí, Eduardo"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"full_name":"Plačková, Lenka","first_name":"Lenka","last_name":"Plačková"},{"last_name":"Opassathian","first_name":"Korawit","full_name":"Opassathian, Korawit"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Doležal, Karel","first_name":"Karel","last_name":"Doležal"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"full_name":"Turnbull, Colin","first_name":"Colin","last_name":"Turnbull"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","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.","year":"2020","month":"08","publication_identifier":{"eissn":["20411723"]},"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17700-9","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000567931000001"]},"oa":1},{"publication_status":"submitted","department":[{"_id":"StFr"}],"publisher":"IST Austria","year":"2020","date_created":"2020-06-30T07:37:39Z","date_updated":"2023-08-22T09:20:36Z","author":[{"last_name":"Varzi","first_name":"Alberto","full_name":"Varzi, Alberto"},{"full_name":"Thanner, Katharina","first_name":"Katharina","last_name":"Thanner"},{"last_name":"Scipioni","first_name":"Roberto","full_name":"Scipioni, Roberto"},{"last_name":"Di Lecce","first_name":"Daniele","full_name":"Di Lecce, Daniele"},{"full_name":"Hassoun, Jusef","last_name":"Hassoun","first_name":"Jusef"},{"first_name":"Susanne","last_name":"Dörfler","full_name":"Dörfler, Susanne"},{"first_name":"Holger","last_name":"Altheus","full_name":"Altheus, Holger"},{"full_name":"Kaskel, Stefan","last_name":"Kaskel","first_name":"Stefan"},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"8361"}]},"file_date_updated":"2020-07-14T12:48:08Z","oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8067","month":"07","publication_identifier":{"issn":["2664-1690"]},"status":"public","ddc":["540"],"title":"Current status and future perspectives of Lithium metal batteries","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"8067","oa_version":"Published Version","file":[{"file_name":"20200612_JPS_review_Li_metal_submitted.pdf","access_level":"open_access","creator":"dernst","file_size":2612498,"content_type":"application/pdf","file_id":"8076","relation":"main_file","date_created":"2020-07-02T07:36:04Z","date_updated":"2020-07-14T12:48:08Z","checksum":"d183ca1465a1cbb4f8db27875cd156f7"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","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."}],"page":"63","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.","mla":"Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067.","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.","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.","ieee":"A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria.","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"},"date_published":"2020-07-01T00:00:00Z","keyword":["Battery","Lithium metal","Lithium-sulphur","Lithium-air","All-solid-state"],"day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"type":"journal_article","issue":"12","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"}],"intvolume":" 480","title":"Current status and future perspectives of lithium metal batteries","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8361","oa_version":"Published Version","article_processing_charge":"No","day":"31","article_type":"original","citation":{"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","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","ieee":"A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020.","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.","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).","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.","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."},"publication":"Journal of Power Sources","date_published":"2020-12-31T00:00:00Z","article_number":"228803","department":[{"_id":"StFr"}],"publisher":"Elsevier","publication_status":"published","year":"2020","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.","volume":480,"date_created":"2020-09-10T10:48:40Z","date_updated":"2023-08-22T09:20:37Z","related_material":{"record":[{"id":"8067","relation":"earlier_version","status":"public"}]},"author":[{"orcid":"0000-0001-5069-0589","first_name":"Alberto","last_name":"Varzi","full_name":"Varzi, Alberto"},{"full_name":"Thanner, Katharina","last_name":"Thanner","first_name":"Katharina","orcid":"0000-0001-5394-2323"},{"full_name":"Scipioni, Roberto","orcid":"0000-0003-1926-421X","last_name":"Scipioni","first_name":"Roberto"},{"last_name":"Di Lecce","first_name":"Daniele","full_name":"Di Lecce, Daniele"},{"full_name":"Hassoun, Jusef","first_name":"Jusef","last_name":"Hassoun"},{"first_name":"Susanne","last_name":"Dörfler","full_name":"Dörfler, Susanne"},{"last_name":"Altheus","first_name":"Holger","full_name":"Altheus, Holger"},{"full_name":"Kaskel, Stefan","last_name":"Kaskel","first_name":"Stefan"},{"orcid":"0000-0003-0654-0940","last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"publication_identifier":{"issn":["0378-7753"]},"month":"12","isi":1,"quality_controlled":"1","external_id":{"isi":["000593857300001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jpowsour.2020.228803"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jpowsour.2020.228803"},{"extern":"1","abstract":[{"text":"The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization.","lang":"eng"}],"type":"preprint","date_created":"2023-08-10T06:47:45Z","date_updated":"2023-08-22T09:17:34Z","oa_version":"Preprint","author":[{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"}],"status":"public","publication_status":"submitted","title":"Attosecond molecular spectroscopy and dynamics","_id":"14028","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","day":"01","month":"02","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-02-01T00:00:00Z","doi":"10.48550/arXiv.2002.02111","page":"2002.02111","oa":1,"citation":{"short":"D.R. 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Springer Nature. 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.","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","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.","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).","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."},"date_published":"2020-09-08T00:00:00Z","type":"journal_article","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"}],"ddc":["530"],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","status":"public","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8529","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1002818,"creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Arnold.pdf","checksum":"88f92544889eb18bb38e25629a422a86","success":1,"date_created":"2020-09-18T13:02:37Z","date_updated":"2020-09-18T13:02:37Z","relation":"main_file","file_id":"8530"}],"month":"09","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","isi":1,"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000577280200001"]},"acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-18269-z","article_number":"4460","file_date_updated":"2020-09-18T13:02:37Z","ec_funded":1,"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","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).","year":"2020","date_updated":"2023-08-22T09:27:12Z","date_created":"2020-09-18T10:56:20Z","volume":11,"author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold","full_name":"Arnold, Georg M"},{"full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","first_name":"William J"},{"full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"13056","status":"public","relation":"research_data"}],"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}]}},{"file":[{"file_id":"8541","relation":"main_file","date_created":"2020-09-21T07:51:44Z","date_updated":"2020-09-21T07:51:44Z","success":1,"checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_name":"2020_ACM_Skrivan.pdf","access_level":"open_access","creator":"dernst","file_size":20223953,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8535","ddc":["000"],"status":"public","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","intvolume":" 39","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"}],"issue":"4","type":"journal_article","date_published":"2020-07-08T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"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.","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.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","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.","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","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. 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ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466"},"article_type":"original","day":"08","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Andreas","last_name":"Soderstrom","full_name":"Soderstrom, Andreas"},{"last_name":"Johansson","first_name":"John","full_name":"Johansson, John"},{"full_name":"Sprenger, Christoph","last_name":"Sprenger","first_name":"Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"date_updated":"2023-08-22T09:28:27Z","date_created":"2020-09-20T22:01:37Z","volume":39,"year":"2020","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.","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"file_date_updated":"2020-09-21T07:51:44Z","ec_funded":1,"article_number":"65","doi":"10.1145/3386569.3392466","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000583700300038"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"07","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]}},{"doi":"10.24033/asens.2431","language":[{"iso":"eng"}],"external_id":{"isi":["000592182600004"],"arxiv":["1708.08013"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"oa":1,"quality_controlled":"1","isi":1,"month":"06","publication_identifier":{"issn":["0012-9593"]},"author":[{"last_name":"Su","first_name":"C.","full_name":"Su, C."},{"full_name":"Zhao, Gufang","last_name":"Zhao","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhong, C.","last_name":"Zhong","first_name":"C."}],"date_updated":"2023-08-22T09:27:57Z","date_created":"2020-09-20T22:01:38Z","volume":53,"year":"2020","publication_status":"published","publisher":"Société Mathématique de France","department":[{"_id":"TaHa"}],"date_published":"2020-06-01T00:00:00Z","publication":"Annales Scientifiques de l'Ecole Normale Superieure","citation":{"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.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","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.","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.","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","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.","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"},"article_type":"original","page":"663-671","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"8539","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"On the K-theory stable bases of the springer resolution","status":"public","intvolume":" 53","abstract":[{"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":"eng"},{"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. "}],"issue":"3","type":"journal_article"},{"citation":{"ama":"Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy. In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics. 1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x","ieee":"D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,” in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and M. Quack, Eds. Elsevier, 2020, pp. 113–161.","apa":"Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x","ista":"Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy. In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.","short":"D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161.","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61, doi:10.1016/b978-0-12-817234-6.00009-x.","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-817234-6.00009-x."},"publication":"Molecular Spectroscopy and Quantum Dynamics","page":"113-161","quality_controlled":"1","doi":"10.1016/b978-0-12-817234-6.00009-x","date_published":"2020-09-25T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9780128172353"],"eisbn":["0128172355"]},"day":"25","month":"09","_id":"14000","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publisher":"Elsevier","editor":[{"last_name":"Marquardt","first_name":"Roberto","full_name":"Marquardt, Roberto"},{"full_name":"Quack, Martin","first_name":"Martin","last_name":"Quack"}],"status":"public","publication_status":"published","title":"Attosecond Molecular Dynamics and Spectroscopy","edition":"1","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"oa_version":"None","date_updated":"2023-08-22T09:25:07Z","date_created":"2023-08-09T13:10:23Z","type":"book_chapter","abstract":[{"lang":"eng","text":"This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented."}],"extern":"1"},{"date_published":"2020-07-27T00:00:00Z","doi":"10.5281/ZENODO.3961561","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"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.” 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).","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","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","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.","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"},"oa":1,"month":"07","day":"27","article_processing_charge":"No","date_updated":"2023-08-22T09:27:11Z","date_created":"2023-05-23T13:37:41Z","oa_version":"Published Version","author":[{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold"},{"first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"full_name":"Hease, William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","first_name":"William J"},{"last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"ddc":["530"],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","status":"public","publisher":"Zenodo","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13056","year":"2020","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."}],"type":"research_data_reference"},{"external_id":{"isi":["000581446000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3390/membranes10090242","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20770375"]},"month":"09","year":"2020","department":[{"_id":"LeSa"}],"publisher":"MDPI","publication_status":"published","author":[{"full_name":"Andrei, Andreea","first_name":"Andreea","last_name":"Andrei"},{"first_name":"Yavuz","last_name":"Öztürk","full_name":"Öztürk, Yavuz"},{"last_name":"Khalfaoui-Hassani","first_name":"Bahia","full_name":"Khalfaoui-Hassani, Bahia"},{"first_name":"Juna","last_name":"Rauch","full_name":"Rauch, Juna"},{"full_name":"Marckmann, Dorian","first_name":"Dorian","last_name":"Marckmann"},{"full_name":"Trasnea, Petru Iulian","id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Petru Iulian","last_name":"Trasnea"},{"last_name":"Daldal","first_name":"Fevzi","full_name":"Daldal, Fevzi"},{"full_name":"Koch, Hans-Georg","last_name":"Koch","first_name":"Hans-Georg"}],"volume":10,"date_created":"2020-09-28T08:59:26Z","date_updated":"2023-08-22T09:34:06Z","article_number":"242","file_date_updated":"2020-09-28T11:36:50Z","citation":{"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.","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","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","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.","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.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020)."},"publication":"Membranes","article_type":"original","date_published":"2020-09-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8579","intvolume":" 10","status":"public","ddc":["570"],"title":"Cu homeostasis in bacteria: The ins and outs","file":[{"relation":"main_file","file_id":"8583","checksum":"ceb43d7554e712dea6f36f9287271737","success":1,"date_updated":"2020-09-28T11:36:50Z","date_created":"2020-09-28T11:36:50Z","access_level":"open_access","file_name":"2020_Membranes_Andrei.pdf","content_type":"application/pdf","file_size":4612258,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"9","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."}]},{"volume":27,"date_updated":"2023-08-22T09:33:09Z","date_created":"2020-09-28T08:59:27Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"author":[{"last_name":"Pinke","first_name":"Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","full_name":"Pinke, Gergely"},{"id":"3E751364-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1864-8951","first_name":"Long","last_name":"Zhou","full_name":"Zhou, Long"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"LeSa"}],"publication_status":"published","pmid":1,"year":"2020","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.","publication_identifier":{"issn":["15459993"],"eissn":["15459985"]},"month":"11","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"doi":"10.1038/s41594-020-0503-8","quality_controlled":"1","isi":1,"external_id":{"pmid":["32929284"],"isi":["000569299400004"]},"issue":"11","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"}],"type":"journal_article","oa_version":"None","intvolume":" 27","title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8581","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","page":"1077-1085","article_type":"original","citation":{"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","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.","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","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.","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","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.","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."},"publication":"Nature Structural and Molecular Biology"},{"type":"conference","article_number":"9158054","abstract":[{"lang":"eng","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."}],"department":[{"_id":"HeEd"}],"publisher":"IEEE","title":"The application of persistent homology in the analysis of heart rate variability","publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8580","year":"2020","oa_version":"None","date_created":"2020-09-28T08:59:27Z","date_updated":"2023-08-22T09:33:34Z","author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","first_name":"Grzegorz"},{"last_name":"Narkiewicz","first_name":"Krzysztof","full_name":"Narkiewicz, Krzysztof"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781728157511"]},"day":"01","month":"08","isi":1,"quality_controlled":"1","external_id":{"isi":["000621172600045"]},"citation":{"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.","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.","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.","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","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.","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","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."},"publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","language":[{"iso":"eng"}],"date_published":"2020-08-01T00:00:00Z","doi":"10.1109/ESGCO49734.2020.9158054","conference":{"start_date":"2020-07-15","location":"Pisa, Italy","end_date":"2020-07-15","name":"ESGCO: European Study Group on Cardiovascular Oscillations"}},{"date_published":"2020-11-04T00:00:00Z","article_type":"original","citation":{"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.","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).","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.","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","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.","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.","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"},"publication":"Advanced Science","has_accepted_license":"1","article_processing_charge":"No","day":"04","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"oa_version":"Published Version","file":[{"success":1,"checksum":"92818c23ecc70e35acfa671f3cfb9909","date_updated":"2020-12-10T14:07:24Z","date_created":"2020-12-10T14:07:24Z","file_id":"8938","relation":"main_file","creator":"dernst","file_size":7835833,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_AdvScience_Tian.pdf"}],"intvolume":" 7","ddc":["570"],"status":"public","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","_id":"8592","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"21","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"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1002/advs.202001724","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000573860700001"]},"publication_identifier":{"issn":["2198-3844"]},"month":"11","volume":7,"date_updated":"2023-08-22T09:53:01Z","date_created":"2020-10-01T09:44:13Z","author":[{"last_name":"Tian","first_name":"Anhao","full_name":"Tian, Anhao"},{"full_name":"Kang, Bo","first_name":"Bo","last_name":"Kang"},{"last_name":"Li","first_name":"Baizhou","full_name":"Li, Baizhou"},{"last_name":"Qiu","first_name":"Biying","full_name":"Qiu, Biying"},{"full_name":"Jiang, Wenhong","first_name":"Wenhong","last_name":"Jiang"},{"full_name":"Shao, Fangjie","first_name":"Fangjie","last_name":"Shao"},{"full_name":"Gao, Qingqing","first_name":"Qingqing","last_name":"Gao"},{"full_name":"Liu, Rui","first_name":"Rui","last_name":"Liu"},{"full_name":"Cai, Chengwei","last_name":"Cai","first_name":"Chengwei"},{"last_name":"Jing","first_name":"Rui","full_name":"Jing, Rui"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","first_name":"Qinghui","last_name":"Liang"},{"last_name":"Bao","first_name":"Lili","full_name":"Bao, Lili"},{"full_name":"Man, Jianghong","first_name":"Jianghong","last_name":"Man"},{"first_name":"Yan","last_name":"Wang","full_name":"Wang, Yan"},{"first_name":"Yu","last_name":"Shi","full_name":"Shi, Yu"},{"full_name":"Li, Jin","first_name":"Jin","last_name":"Li"},{"first_name":"Minmin","last_name":"Yang","full_name":"Yang, Minmin"},{"last_name":"Wang","first_name":"Lisha","full_name":"Wang, Lisha"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Zhu, Junming","first_name":"Junming","last_name":"Zhu"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"last_name":"Wang","first_name":"Ying‐Jie","full_name":"Wang, Ying‐Jie"},{"full_name":"Liu, Chong","first_name":"Chong","last_name":"Liu"}],"department":[{"_id":"SiHi"}],"publisher":"Wiley","publication_status":"published","year":"2020","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.","ec_funded":1,"file_date_updated":"2020-12-10T14:07:24Z","article_number":"2001724"},{"date_published":"2020-09-24T00:00:00Z","citation":{"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","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","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.","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","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.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","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."},"publication":"Nature Communications","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"24","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file":[{"creator":"dernst","file_size":1822469,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Prehal.pdf","success":1,"checksum":"eada7bc8dd16a49390137cff882ef328","date_created":"2020-09-28T13:16:15Z","date_updated":"2020-09-28T13:16:15Z","file_id":"8585","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8568","intvolume":" 11","ddc":["530"],"status":"public","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","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."}],"type":"journal_article","doi":"10.1038/s41467-020-18610-6","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000573756600004"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"month":"09","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"last_name":"Fitzek","first_name":"Harald","full_name":"Fitzek, Harald"},{"full_name":"Kothleitner, Gerald","first_name":"Gerald","last_name":"Kothleitner"},{"first_name":"Volker","last_name":"Presser","full_name":"Presser, Volker"},{"last_name":"Gollas","first_name":"Bernhard","full_name":"Gollas, Bernhard"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"},{"last_name":"Abbas","first_name":"Qamar","full_name":"Abbas, Qamar"}],"volume":11,"date_created":"2020-09-25T07:23:13Z","date_updated":"2023-08-22T09:37:24Z","year":"2020","department":[{"_id":"StFr"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-09-28T13:16:15Z","article_number":"4838"},{"date_updated":"2023-08-22T09:58:21Z","date_created":"2020-10-11T22:01:14Z","volume":10,"author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"full_name":"Carrasco, Denisse","first_name":"Denisse","last_name":"Carrasco"},{"last_name":"Lopez-Jury","first_name":"Luciana","full_name":"Lopez-Jury, Luciana"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"first_name":"Natalia","last_name":"Marquez","full_name":"Marquez, Natalia"},{"last_name":"Mpodozis","first_name":"Jorge","full_name":"Mpodozis, Jorge"},{"last_name":"Marin","first_name":"Gonzalo","full_name":"Marin, Gonzalo"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaJö"}],"year":"2020","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.).","file_date_updated":"2020-10-12T12:39:10Z","article_number":"16220","language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-72848-0","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577142600032"]},"oa":1,"month":"10","publication_identifier":{"eissn":["20452322"]},"oa_version":"Published Version","file":[{"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1,"date_updated":"2020-10-12T12:39:10Z","date_created":"2020-10-12T12:39:10Z","relation":"main_file","file_id":"8651","content_type":"application/pdf","file_size":3906744,"creator":"dernst","access_level":"open_access","file_name":"2020_ScientificReport_Deichler.pdf"}],"status":"public","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":["570"],"intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8643","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2020-10-01T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"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","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.","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","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.","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.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","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."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"month":"03","doi":"10.1093/bioinformatics/btz841","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-10-12T12:02:09Z","author":[{"last_name":"Esteban","first_name":"Laura A","full_name":"Esteban, Laura A"},{"full_name":"Lonishin, Lyubov R","last_name":"Lonishin","first_name":"Lyubov R"},{"full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M","last_name":"Bobrovskiy"},{"last_name":"Leleytner","first_name":"Gregory","full_name":"Leleytner, Gregory"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Ivankov, Dmitry N ","first_name":"Dmitry N ","last_name":"Ivankov"}],"volume":36,"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:57:29Z","pmid":1,"year":"2020","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). ","department":[{"_id":"FyKo"}],"publisher":"Oxford Academic","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2020-03-15T00:00:00Z","citation":{"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","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.","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.","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","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.","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.","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."},"publication":"Bioinformatics","page":"1960-1962","article_type":"original","issue":"6","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2020-10-12T12:02:09Z","date_updated":"2020-10-12T12:02:09Z","success":1,"checksum":"21d6f71839deb3b83e4a356193f72767","file_id":"8649","relation":"main_file","creator":"dernst","file_size":308341,"content_type":"application/pdf","file_name":"2020_Bioinformatics_Esteban.pdf","access_level":"open_access"}],"_id":"8645","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 36","ddc":["000","570"],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","status":"public"},{"scopus_import":"1","day":"23","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","publication":"Physical Biology","citation":{"short":"J. Merrin, Physical Biology 17 (2020).","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.","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.","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","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","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.","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005."},"date_published":"2020-09-23T00:00:00Z","type":"journal_article","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"}],"issue":"6","title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","ddc":["510","570"],"status":"public","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8597","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1667111,"file_name":"2020_PhysBio_Merrin.pdf","access_level":"open_access","date_updated":"2020-10-05T13:53:59Z","date_created":"2020-10-05T13:53:59Z","success":1,"checksum":"fec9bdd355ed349f09990faab20838a7","file_id":"8609","relation":"main_file"}],"oa_version":"Published Version","month":"09","publication_identifier":{"eissn":["14783975"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000575539700001"]},"language":[{"iso":"eng"}],"doi":"10.1088/1478-3975/abb2db","article_number":"065005","file_date_updated":"2020-10-05T13:53:59Z","publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"IOP Publishing","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.","year":"2020","date_updated":"2023-08-22T09:53:29Z","date_created":"2020-10-04T22:01:35Z","volume":17,"author":[{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"}]},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","page":"P919-936.E11","article_type":"original","citation":{"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","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.","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.","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","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.","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.","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."},"publication":"Neuron","date_published":"2020-12-09T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"lang":"eng","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."}],"intvolume":" 108","ddc":["570"],"title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8674","file":[{"file_id":"8939","relation":"main_file","success":1,"checksum":"054562bb50165ef9a1f46631c1c5e36b","date_created":"2020-12-10T14:42:09Z","date_updated":"2020-12-10T14:42:09Z","access_level":"open_access","file_name":"2020_Neuron_Henneberger.pdf","creator":"dernst","file_size":7518960,"content_type":"application/pdf"}],"oa_version":"Published Version","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"month":"12","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32976770"],"isi":["000603428000010"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2020.08.030","file_date_updated":"2020-12-10T14:42:09Z","publisher":"Elsevier","department":[{"_id":"HaJa"}],"publication_status":"published","pmid":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.).","year":"2020","volume":108,"date_created":"2020-10-18T22:01:38Z","date_updated":"2023-08-22T09:59:29Z","author":[{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"first_name":"Lucie","last_name":"Bard","full_name":"Bard, Lucie"},{"full_name":"Panatier, Aude","first_name":"Aude","last_name":"Panatier"},{"full_name":"Reynolds, James P.","first_name":"James P.","last_name":"Reynolds"},{"first_name":"Olga","last_name":"Kopach","full_name":"Kopach, Olga"},{"last_name":"Medvedev","first_name":"Nikolay I.","full_name":"Medvedev, Nikolay I."},{"last_name":"Minge","first_name":"Daniel","full_name":"Minge, Daniel"},{"full_name":"Herde, Michel K.","last_name":"Herde","first_name":"Michel K."},{"first_name":"Stefanie","last_name":"Anders","full_name":"Anders, Stefanie"},{"last_name":"Kraev","first_name":"Igor","full_name":"Kraev, Igor"},{"full_name":"Heller, Janosch P.","last_name":"Heller","first_name":"Janosch P."},{"full_name":"Rama, Sylvain","first_name":"Sylvain","last_name":"Rama"},{"full_name":"Zheng, Kaiyu","first_name":"Kaiyu","last_name":"Zheng"},{"first_name":"Thomas P.","last_name":"Jensen","full_name":"Jensen, Thomas P."},{"full_name":"Sanchez-Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez-Romero","first_name":"Inmaculada"},{"last_name":"Jackson","first_name":"Colin J.","full_name":"Jackson, Colin J."},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Ottersen, Ole Petter","last_name":"Ottersen","first_name":"Ole Petter"},{"last_name":"Nagelhus","first_name":"Erlend Arnulf","full_name":"Nagelhus, Erlend Arnulf"},{"last_name":"Oliet","first_name":"Stephane H.R.","full_name":"Oliet, Stephane H.R."},{"full_name":"Stewart, Michael G.","last_name":"Stewart","first_name":"Michael G."},{"last_name":"Nägerl","first_name":"U. VAlentin","full_name":"Nägerl, U. VAlentin"},{"full_name":"Rusakov, Dmitri A. ","first_name":"Dmitri A. ","last_name":"Rusakov"}]},{"title":"Filtering spins by scattering from a lattice of point magnets","ddc":["530"],"status":"public","intvolume":" 3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8652","file":[{"success":1,"checksum":"60cd35b99f0780acffc7b6060e49ec8b","date_created":"2020-10-14T15:16:28Z","date_updated":"2020-10-14T15:16:28Z","file_id":"8662","relation":"main_file","creator":"dernst","file_size":1462934,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_CommPhysics_Ghazaryan.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"article_type":"original","publication":"Communications Physics","citation":{"ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","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.","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)."},"date_published":"2020-10-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"Yes","has_accepted_license":"1","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Springer Nature","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).","year":"2020","date_updated":"2023-08-22T09:58:46Z","date_created":"2020-10-13T09:48:59Z","volume":3,"author":[{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"article_number":"178","file_date_updated":"2020-10-14T15:16:28Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"external_id":{"isi":["000581681000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s42005-020-00445-8","month":"10","publication_identifier":{"issn":["2399-3650"]}},{"doi":"10.1038/s41467-020-18837-3","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577244600003"],"pmid":["33028844"]},"quality_controlled":"1","isi":1,"month":"10","publication_identifier":{"eissn":["20411723"]},"author":[{"last_name":"Sznurkowska","first_name":"Magdalena K.","full_name":"Sznurkowska, Magdalena K."},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Azzarelli, Roberta","last_name":"Azzarelli","first_name":"Roberta"},{"full_name":"Chatzeli, Lemonia","last_name":"Chatzeli","first_name":"Lemonia"},{"full_name":"Ikeda, Tatsuro","first_name":"Tatsuro","last_name":"Ikeda"},{"full_name":"Yoshida, Shosei","last_name":"Yoshida","first_name":"Shosei"},{"first_name":"Anna","last_name":"Philpott","full_name":"Philpott, Anna"},{"full_name":"Simons, Benjamin D","last_name":"Simons","first_name":"Benjamin D"}],"date_updated":"2023-08-22T10:18:17Z","date_created":"2020-10-18T22:01:35Z","volume":11,"year":"2020","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"file_date_updated":"2020-10-19T11:27:46Z","article_number":"5037","date_published":"2020-10-07T00:00:00Z","publication":"Nature Communications","citation":{"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","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","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.","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","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.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (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."},"article_type":"original","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"success":1,"checksum":"0ecc0eab72d2d50694852579611a6624","date_created":"2020-10-19T11:27:46Z","date_updated":"2020-10-19T11:27:46Z","file_id":"8677","relation":"main_file","creator":"dernst","file_size":5540540,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Sznurkowska.pdf"}],"oa_version":"Published Version","_id":"8669","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Tracing the cellular basis of islet specification in mouse pancreas","intvolume":" 11","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."}],"type":"journal_article"},{"file":[{"checksum":"88e1a031a61689165d19a19c2f16d795","success":1,"date_updated":"2021-02-04T10:20:02Z","date_created":"2021-02-04T10:20:02Z","relation":"main_file","file_id":"9086","file_size":6929686,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_DevelopmCell_Chaigne.pdf"}],"oa_version":"Published Version","_id":"8672","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 55","status":"public","ddc":["570"],"title":"Abscission couples cell division to embryonic stem cell fate","issue":"2","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2020-10-26T00:00:00Z","citation":{"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","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.","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","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.","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.","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.","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."},"publication":"Developmental Cell","page":"195-208","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"26","scopus_import":"1","author":[{"first_name":"Agathe","last_name":"Chaigne","full_name":"Chaigne, Agathe"},{"last_name":"Labouesse","first_name":"Céline","full_name":"Labouesse, Céline"},{"first_name":"Ian J.","last_name":"White","full_name":"White, Ian J."},{"full_name":"Agnew, Meghan","last_name":"Agnew","first_name":"Meghan"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chalut, Kevin J.","last_name":"Chalut","first_name":"Kevin J."},{"full_name":"Paluch, Ewa K.","last_name":"Paluch","first_name":"Ewa K."}],"volume":55,"date_created":"2020-10-18T22:01:37Z","date_updated":"2023-08-22T10:16:58Z","pmid":1,"year":"2020","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).","department":[{"_id":"EdHa"}],"publisher":"Elsevier","publication_status":"published","file_date_updated":"2021-02-04T10:20:02Z","doi":"10.1016/j.devcel.2020.09.001","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"month":"10"},{"date_updated":"2023-08-22T10:38:38Z","date_created":"2020-10-25T23:01:16Z","volume":33,"author":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael","full_name":"Kniely, Michael"}],"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"IOP Publishing","year":"2020","license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2020-10-27T12:09:57Z","language":[{"iso":"eng"}],"doi":"10.1088/1361-6544/ab9728","quality_controlled":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000576492700001"],"arxiv":["1906.12245"]},"month":"11","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"oa_version":"Published Version","file":[{"file_name":"2020_Nonlinearity_Fischer.pdf","access_level":"open_access","creator":"cziletti","file_size":1223899,"content_type":"application/pdf","file_id":"8710","relation":"main_file","date_created":"2020-10-27T12:09:57Z","date_updated":"2020-10-27T12:09:57Z","success":1,"checksum":"ed90bc6eb5f32ee6157fef7f3aabc057"}],"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","ddc":["510"],"status":"public","intvolume":" 33","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8697","abstract":[{"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.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2020-11-01T00:00:00Z","article_type":"original","page":"5733-5772","publication":"Nonlinearity","citation":{"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.","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.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","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.","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.","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"},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1126/science.aba6637","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"external_id":{"isi":["000579169000053"]},"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"10","volume":370,"date_updated":"2023-08-22T10:36:35Z","date_created":"2020-10-19T14:09:38Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/sticking-together/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Tsai, Tony Y.-C.","first_name":"Tony Y.-C.","last_name":"Tsai"},{"last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng"},{"full_name":"Colak-Champollion, Tugba","first_name":"Tugba","last_name":"Colak-Champollion"},{"full_name":"Knaut, Holger","first_name":"Holger","last_name":"Knaut"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Sean G.","last_name":"Megason","full_name":"Megason, Sean G."}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"publication_status":"published","year":"2020","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.).","ec_funded":1,"date_published":"2020-10-02T00:00:00Z","page":"113-116","article_type":"original","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.","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.","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.","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","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.","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","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."},"publication":"Science","article_processing_charge":"No","day":"02","keyword":["Multidisciplinary"],"scopus_import":"1","oa_version":"Preprint","intvolume":" 370","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","status":"public","_id":"8680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6512","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"oa_version":"None","intvolume":" 52","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8707","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"}],"type":"journal_article","date_published":"2020-10-19T00:00:00Z","page":"1247-1255","article_type":"original","citation":{"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.","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.","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","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.","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"},"publication":"Nature Genetics","article_processing_charge":"No","day":"19","scopus_import":"1","volume":52,"date_created":"2020-10-25T23:01:20Z","date_updated":"2023-08-22T10:37:10Z","author":[{"full_name":" Galan, Silvia","first_name":"Silvia","last_name":" Galan"},{"full_name":"Machnik, Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742","first_name":"Nick N","last_name":"Machnik"},{"last_name":"Kruse","first_name":"Kai","full_name":"Kruse, Kai"},{"full_name":"Díaz, Noelia","last_name":"Díaz","first_name":"Noelia"},{"last_name":"Marti-Renom","first_name":"Marc A","full_name":"Marti-Renom, Marc A"},{"last_name":"Vaquerizas","first_name":"Juan M","full_name":"Vaquerizas, Juan M"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2020","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.","language":[{"iso":"eng"}],"doi":"10.1038/s41588-020-00712-y","isi":1,"quality_controlled":"1","external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"publication_identifier":{"eissn":["15461718"],"issn":["10614036"]},"month":"10"},{"article_type":"original","page":"642-652","publication":"Nature Machine Intelligence","citation":{"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.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652.","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.","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","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.","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.","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"},"date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Neural circuit policies enabling auditable autonomy","status":"public","intvolume":" 2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8679","oa_version":"None","type":"journal_article","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."}],"quality_controlled":"1","isi":1,"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000583337200011"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42256-020-00237-3","month":"10","publication_identifier":{"eissn":["2522-5839"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"year":"2020","date_updated":"2023-08-22T10:36:06Z","date_created":"2020-10-19T13:46:06Z","volume":2,"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-deep-learning-models/"}]}},{"date_published":"2020-10-01T00:00:00Z","citation":{"short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","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.","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.","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","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.","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201."},"publication":"Journal of Mathematical Physics","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"8670","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 61","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","status":"public","issue":"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)]."}],"type":"journal_article","doi":"10.1063/5.0022787","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06644"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00222488"]},"month":"10","author":[{"full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","last_name":"Zhang"}],"volume":61,"date_updated":"2023-08-22T10:32:29Z","date_created":"2020-10-18T22:01:36Z","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.","year":"2020","publisher":"AIP Publishing","department":[{"_id":"JaMa"}],"publication_status":"published","ec_funded":1,"article_number":"102201"},{"abstract":[{"lang":"eng","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."}],"issue":"40","type":"journal_article","file":[{"file_name":"2020_PNAS_Maoz.pdf","access_level":"open_access","file_size":1755359,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8713","date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","checksum":"c6a24fdecf3f28faf447078e7a274a88","success":1}],"oa_version":"Published Version","_id":"8698","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Learning probabilistic neural representations with randomly connected circuits","status":"public","intvolume":" 117","day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-10-06T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","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.","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.","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.","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","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.","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","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."},"article_type":"original","page":"25066-25073","file_date_updated":"2020-10-27T14:57:50Z","author":[{"full_name":"Maoz, Ori","last_name":"Maoz","first_name":"Ori"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"first_name":"Mohamad Saleh","last_name":"Esteki","full_name":"Esteki, Mohamad Saleh"},{"first_name":"Roozbeh","last_name":"Kiani","full_name":"Kiani, Roozbeh"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"date_created":"2020-10-25T23:01:16Z","date_updated":"2023-08-22T12:11:23Z","volume":117,"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.).","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","month":"10","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"doi":"10.1073/pnas.1912804117","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"quality_controlled":"1","isi":1},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"5446-5452","citation":{"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.","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.","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","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.","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","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.","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"},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","date_published":"2020-05-01T00:00:00Z","alternative_title":["ICRA"],"type":"conference","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"}],"status":"public","title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","ddc":["000"],"_id":"8704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":1070010,"creator":"dernst","access_level":"open_access","file_name":"2020_ICRA_Lechner.pdf","checksum":"fccf7b986ac78046918a298cc6849a50","success":1,"date_updated":"2020-11-06T10:58:49Z","date_created":"2020-11-06T10:58:49Z","relation":"main_file","file_id":"8733"}],"oa_version":"Submitted Version","publication_identifier":{"issn":["10504729"],"isbn":["9781728173955"]},"month":"05","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000712319503110"]},"language":[{"iso":"eng"}],"doi":"10.1109/ICRA40945.2020.9196608","conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2020-08-31","start_date":"2020-05-31","location":"Paris, France"},"file_date_updated":"2020-11-06T10:58:49Z","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","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.","year":"2020","date_created":"2020-10-25T23:01:19Z","date_updated":"2023-08-22T10:40:15Z","author":[{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}]},{"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"}],"issue":"5","type":"journal_article","oa_version":"None","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","status":"public","intvolume":" 54","_id":"8700","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-09-01T00:00:00Z","article_type":"original","page":"739-748","publication":"Molecular Biology","citation":{"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.","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.","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","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.","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.","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"},"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T10:39:38Z","volume":54,"author":[{"last_name":"Sokolova","first_name":"E. E.","full_name":"Sokolova, E. E."},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"last_name":"Shuvalov","first_name":"A. V.","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"related_material":{"record":[{"relation":"original","status":"public","id":"8701"}]},"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","year":"2020","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.","month":"09","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"language":[{"iso":"eng"}],"doi":"10.1134/S0026893320050088","isi":1,"quality_controlled":"1","external_id":{"isi":["000579441200009"]}},{"publication_identifier":{"issn":["00268984"]},"month":"09","external_id":{"pmid":["33009793"]},"quality_controlled":"1","doi":"10.31857/S0026898420050080","language":[{"iso":"rus"}],"pmid":1,"year":"2020","department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","publication_status":"published","related_material":{"record":[{"id":"8700","relation":"translation","status":"public"}]},"author":[{"first_name":"E. E.","last_name":"Sokolova","full_name":"Sokolova, E. E."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Shuvalov, A. V.","last_name":"Shuvalov","first_name":"A. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"volume":54,"date_updated":"2023-08-22T10:39:37Z","date_created":"2020-10-25T23:01:17Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 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","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.","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.","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"},"publication":"Molekuliarnaia biologiia","page":"837-848","article_type":"original","date_published":"2020-09-01T00:00:00Z","type":"journal_article","issue":"5","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"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8701","intvolume":" 54","status":"public","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","oa_version":"None"},{"article_processing_charge":"No","day":"12","month":"11","date_published":"2020-11-12T00:00:00Z","doi":"10.48550/arXiv.2011.06630","language":[{"iso":"eng"}],"external_id":{"arxiv":["2011.06630"]},"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.","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.).","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. .","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","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.","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"oa":1,"publication":"arXiv","abstract":[{"lang":"eng","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."}],"type":"preprint","article_number":"2011.06630","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"},{"last_name":"Everson","first_name":"Rosa Wallace","full_name":"Everson, Rosa Wallace"},{"last_name":"Enrico Ramirez-Ruiz","first_name":"Enrico Ramirez-Ruiz","full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz"},{"full_name":"Mink, Selma E. de","first_name":"Selma E. de","last_name":"Mink"},{"full_name":"Son, Lieke A. C. van","first_name":"Lieke A. C. van","last_name":"Son"},{"first_name":"Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","full_name":"Götberg, 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","first_name":"Mathieu","last_name":"Renzo"},{"last_name":"Wu","first_name":"Samantha","full_name":"Wu, Samantha"},{"full_name":"Schrøder, Sophie L.","first_name":"Sophie L.","last_name":"Schrøder"},{"first_name":"Ryan J.","last_name":"Foley","full_name":"Foley, Ryan J."},{"last_name":"Tenley Hutchinson-Smith","first_name":"Tenley Hutchinson-Smith","full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith"}],"oa_version":"Preprint","date_created":"2023-08-21T10:10:41Z","date_updated":"2023-08-22T11:03:00Z","_id":"14096","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","status":"public","publication_status":"submitted"},{"type":"journal_article","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."}],"issue":"40","ddc":["530"],"title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","status":"public","intvolume":" 117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8699","file":[{"creator":"cziletti","file_size":1176522,"content_type":"application/pdf","file_name":"2020_PNAS_Paris.pdf","access_level":"open_access","date_updated":"2020-10-28T11:53:12Z","date_created":"2020-10-28T11:53:12Z","success":1,"checksum":"1638fa36b442e2868576c6dd7d6dc505","file_id":"8715","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"24764-24770","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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.","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.","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.","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","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.","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","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."},"date_published":"2020-10-06T00:00:00Z","file_date_updated":"2020-10-28T11:53:12Z","ec_funded":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MiLe"}],"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.","year":"2020","pmid":1,"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T12:11:52Z","volume":117,"author":[{"first_name":"Eugenio","last_name":"Paris","full_name":"Paris, Eugenio"},{"first_name":"Yi","last_name":"Tseng","full_name":"Tseng, Yi"},{"id":"8275014E-6063-11E9-9B7F-6338E6697425","orcid":"0000-0003-0853-8182","first_name":"Ekaterina","last_name":"Paerschke","full_name":"Paerschke, Ekaterina"},{"full_name":"Zhang, Wenliang","first_name":"Wenliang","last_name":"Zhang"},{"full_name":"Upton, Mary H","first_name":"Mary H","last_name":"Upton"},{"full_name":"Efimenko, Anna","first_name":"Anna","last_name":"Efimenko"},{"first_name":"Katharina","last_name":"Rolfs","full_name":"Rolfs, Katharina"},{"full_name":"McNally, Daniel E","last_name":"McNally","first_name":"Daniel E"},{"first_name":"Laura","last_name":"Maurel","full_name":"Maurel, Laura"},{"last_name":"Naamneh","first_name":"Muntaser","full_name":"Naamneh, Muntaser"},{"first_name":"Marco","last_name":"Caputo","full_name":"Caputo, Marco"},{"full_name":"Strocov, Vladimir N","first_name":"Vladimir N","last_name":"Strocov"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"full_name":"Casa, Diego","first_name":"Diego","last_name":"Casa"},{"full_name":"Schneider, Christof W","last_name":"Schneider","first_name":"Christof W"},{"full_name":"Pomjakushina, Ekaterina","first_name":"Ekaterina","last_name":"Pomjakushina"},{"last_name":"Wohlfeld","first_name":"Krzysztof","full_name":"Wohlfeld, Krzysztof"},{"last_name":"Radovic","first_name":"Milan","full_name":"Radovic, Milan"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"month":"10","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"external_id":{"arxiv":["2009.12262"],"isi":["000579059100029"],"pmid":["32958669"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2012043117"},{"oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":7618987,"creator":"lsazanov","access_level":"open_access","file_name":"Full_manuscript_with_SI_opt_red.pdf","checksum":"658ba90979ca9528a2efdfac8547047a","success":1,"date_created":"2020-11-26T18:47:58Z","date_updated":"2020-11-26T18:47:58Z","relation":"main_file","file_id":"8820"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8737","intvolume":" 370","ddc":["572"],"status":"public","title":"The coupling mechanism of mammalian respiratory complex I","issue":"6516","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"}],"type":"journal_article","date_published":"2020-10-30T00:00:00Z","citation":{"ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","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","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.","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.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020)."},"publication":"Science","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"volume":370,"date_created":"2020-11-08T23:01:23Z","date_updated":"2023-08-22T12:35:38Z","pmid":1,"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","year":"2020","publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-26T18:47:58Z","article_number":"eabc4209","doi":"10.1126/science.abc4209","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"external_id":{"isi":["000583031800004"],"pmid":["32972993"]},"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["10959203"]},"month":"10"},{"date_published":"2020-02-01T00:00:00Z","publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"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.","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","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.","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","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.","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.","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."},"page":"45-61","day":"01","article_processing_charge":"No","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8722","title":"Taming unbalanced training workloads in deep learning with partial collective operations","status":"public","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"}],"type":"conference","conference":{"end_date":"2020-02-26","location":"San Diego, CA, United States","start_date":"2020-02-22","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3332466.3374528","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.04207"}],"external_id":{"arxiv":["1908.04207"],"isi":["000564476500004"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"month":"02","author":[{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"first_name":"Tal Ben-Nun","last_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun"},{"last_name":"Girolamo","first_name":"Salvatore Di","full_name":"Girolamo, Salvatore Di"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"}],"date_created":"2020-11-05T15:25:30Z","date_updated":"2023-08-22T12:13:48Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"ec_funded":1},{"has_accepted_license":"1","article_processing_charge":"No","day":"04","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","date_published":"2020-11-04T00:00:00Z","article_type":"original","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.","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","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","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","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.","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.","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)."},"publication":"Nature Communications","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"8745","date_updated":"2020-11-09T07:56:24Z","date_created":"2020-11-09T07:56:24Z","checksum":"b2688f0347e69e6629bba582077278c5","success":1,"file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","file_size":1670898,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 11","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","status":"public","ddc":["570"],"_id":"8744","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2041-1723"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19372-x","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000592028600001"]},"file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","volume":11,"date_updated":"2023-08-22T12:36:07Z","date_created":"2020-11-09T07:49:36Z","author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"full_name":"Mao, Jiafei","last_name":"Mao","first_name":"Jiafei"},{"first_name":"Julian","last_name":"Reitz","full_name":"Reitz, Julian"},{"full_name":"Sreeramulu, Sridhar","first_name":"Sridhar","last_name":"Sreeramulu"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Meier-Credo","first_name":"Jakob","full_name":"Meier-Credo, Jakob"},{"full_name":"Saxena, Krishna","first_name":"Krishna","last_name":"Saxena"},{"full_name":"Buhr, Florian","last_name":"Buhr","first_name":"Florian"},{"full_name":"Langer, Julian D.","first_name":"Julian D.","last_name":"Langer"},{"full_name":"Blackledge, Martin","first_name":"Martin","last_name":"Blackledge"},{"full_name":"Frangakis, Achilleas S.","last_name":"Frangakis","first_name":"Achilleas S."},{"last_name":"Glaubitz","first_name":"Clemens","full_name":"Glaubitz, Clemens"},{"last_name":"Schwalbe","first_name":"Harald","full_name":"Schwalbe, Harald"}],"publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"publication_status":"published","year":"2020","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."},{"type":"journal_article","issue":"40","abstract":[{"lang":"eng","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8747","intvolume":" 8","title":"Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks","status":"public","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"28","citation":{"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.","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.","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","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.","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.","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."},"publication":"Journal of Materials Chemistry C","page":"14092-14099","article_type":"original","date_published":"2020-10-28T00:00:00Z","ec_funded":1,"year":"2020","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.","department":[{"_id":"MaIb"}],"publisher":"Royal Society of Chemistry","publication_status":"published","author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"first_name":"Mariano","last_name":"Calcabrini","full_name":"Calcabrini, Mariano"},{"full_name":"Xing, Congcong","first_name":"Congcong","last_name":"Xing"},{"last_name":"Han","first_name":"Xu","full_name":"Han, Xu"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"volume":8,"date_created":"2020-11-09T08:37:51Z","date_updated":"2023-08-22T12:41:05Z","month":"10","external_id":{"isi":["000581559100015"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1039/D0TC02182B","language":[{"iso":"eng"}]},{"publication":"arXiv","citation":{"ama":"Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683","ista":"Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv, 2001.06683.","apa":"Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy, K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683","ieee":"B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission concept study final report,” arXiv. .","mla":"Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683.","short":"B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy, J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin, D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt, C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding, H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian, M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois, C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D. Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett, D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene, J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R. Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist, M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading, J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad, J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi, M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf, K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith, B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras, J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick, D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney, J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek, B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K. Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt, R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L. Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini, P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge, I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J. Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv (n.d.).","chicago":"Gaudi, B. Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683."},"oa":1,"external_id":{"arxiv":["2001.06683"]},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2001.06683","open_access":"1"}],"doi":"10.48550/arXiv.2001.06683","date_published":"2020-01-18T00:00:00Z","language":[{"iso":"eng"}],"day":"18","month":"01","article_processing_charge":"No","year":"2020","_id":"14095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","title":"The habitable exoplanet observatory (HabEx) mission concept study final report","status":"public","author":[{"first_name":"B. Scott","last_name":"Gaudi","full_name":"Gaudi, B. Scott"},{"full_name":"Seager, Sara","last_name":"Seager","first_name":"Sara"},{"full_name":"Mennesson, Bertrand","last_name":"Mennesson","first_name":"Bertrand"},{"first_name":"Alina","last_name":"Kiessling","full_name":"Kiessling, Alina"},{"first_name":"Keith","last_name":"Warfield","full_name":"Warfield, Keith"},{"first_name":"Kerri","last_name":"Cahoy","full_name":"Cahoy, Kerri"},{"full_name":"Clarke, John T.","last_name":"Clarke","first_name":"John T."},{"first_name":"Shawn Domagal-Goldman","last_name":"Shawn Domagal-Goldman","full_name":"Shawn Domagal-Goldman, Shawn Domagal-Goldman"},{"first_name":"Lee","last_name":"Feinberg","full_name":"Feinberg, Lee"},{"first_name":"Olivier","last_name":"Guyon","full_name":"Guyon, Olivier"},{"full_name":"Kasdin, Jeremy","first_name":"Jeremy","last_name":"Kasdin"},{"first_name":"Dimitri","last_name":"Mawet","full_name":"Mawet, Dimitri"},{"last_name":"Plavchan","first_name":"Peter","full_name":"Plavchan, Peter"},{"full_name":"Robinson, Tyler","last_name":"Robinson","first_name":"Tyler"},{"last_name":"Rogers","first_name":"Leslie","full_name":"Rogers, Leslie"},{"last_name":"Scowen","first_name":"Paul","full_name":"Scowen, Paul"},{"full_name":"Somerville, Rachel","first_name":"Rachel","last_name":"Somerville"},{"full_name":"Stapelfeldt, Karl","last_name":"Stapelfeldt","first_name":"Karl"},{"full_name":"Stark, Christopher","first_name":"Christopher","last_name":"Stark"},{"first_name":"Daniel","last_name":"Stern","full_name":"Stern, Daniel"},{"first_name":"Margaret","last_name":"Turnbull","full_name":"Turnbull, Margaret"},{"full_name":"Amini, Rashied","first_name":"Rashied","last_name":"Amini"},{"first_name":"Gary","last_name":"Kuan","full_name":"Kuan, Gary"},{"first_name":"Stefan","last_name":"Martin","full_name":"Martin, Stefan"},{"full_name":"Morgan, Rhonda","first_name":"Rhonda","last_name":"Morgan"},{"first_name":"David","last_name":"Redding","full_name":"Redding, David"},{"full_name":"Stahl, H. Philip","last_name":"Stahl","first_name":"H. Philip"},{"full_name":"Webb, Ryan","last_name":"Webb","first_name":"Ryan"},{"last_name":"Oscar Alvarez-Salazar","first_name":"Oscar Alvarez-Salazar","full_name":"Oscar Alvarez-Salazar, Oscar Alvarez-Salazar"},{"full_name":"Arnold, William L.","first_name":"William L.","last_name":"Arnold"},{"first_name":"Manan","last_name":"Arya","full_name":"Arya, Manan"},{"last_name":"Balasubramanian","first_name":"Bala","full_name":"Balasubramanian, Bala"},{"full_name":"Baysinger, Mike","first_name":"Mike","last_name":"Baysinger"},{"full_name":"Bell, Ray","last_name":"Bell","first_name":"Ray"},{"full_name":"Below, Chris","first_name":"Chris","last_name":"Below"},{"full_name":"Benson, Jonathan","first_name":"Jonathan","last_name":"Benson"},{"last_name":"Blais","first_name":"Lindsey","full_name":"Blais, Lindsey"},{"full_name":"Booth, Jeff","last_name":"Booth","first_name":"Jeff"},{"full_name":"Bourgeois, Robert","first_name":"Robert","last_name":"Bourgeois"},{"first_name":"Case","last_name":"Bradford","full_name":"Bradford, Case"},{"full_name":"Brewer, Alden","first_name":"Alden","last_name":"Brewer"},{"last_name":"Brooks","first_name":"Thomas","full_name":"Brooks, Thomas"},{"full_name":"Cady, Eric","first_name":"Eric","last_name":"Cady"},{"full_name":"Caldwell, Mary","last_name":"Caldwell","first_name":"Mary"},{"full_name":"Calvet, Rob","last_name":"Calvet","first_name":"Rob"},{"first_name":"Steven","last_name":"Carr","full_name":"Carr, Steven"},{"full_name":"Chan, Derek","last_name":"Chan","first_name":"Derek"},{"first_name":"Velibor","last_name":"Cormarkovic","full_name":"Cormarkovic, Velibor"},{"full_name":"Coste, Keith","last_name":"Coste","first_name":"Keith"},{"last_name":"Cox","first_name":"Charlie","full_name":"Cox, Charlie"},{"full_name":"Danner, Rolf","last_name":"Danner","first_name":"Rolf"},{"full_name":"Davis, Jacqueline","last_name":"Davis","first_name":"Jacqueline"},{"first_name":"Larry","last_name":"Dewell","full_name":"Dewell, Larry"},{"full_name":"Dorsett, Lisa","first_name":"Lisa","last_name":"Dorsett"},{"full_name":"Dunn, Daniel","first_name":"Daniel","last_name":"Dunn"},{"last_name":"East","first_name":"Matthew","full_name":"East, Matthew"},{"full_name":"Effinger, Michael","last_name":"Effinger","first_name":"Michael"},{"last_name":"Eng","first_name":"Ron","full_name":"Eng, Ron"},{"first_name":"Greg","last_name":"Freebury","full_name":"Freebury, Greg"},{"full_name":"Garcia, Jay","first_name":"Jay","last_name":"Garcia"},{"full_name":"Gaskin, Jonathan","last_name":"Gaskin","first_name":"Jonathan"},{"full_name":"Greene, Suzan","first_name":"Suzan","last_name":"Greene"},{"last_name":"Hennessy","first_name":"John","full_name":"Hennessy, John"},{"last_name":"Hilgemann","first_name":"Evan","full_name":"Hilgemann, Evan"},{"full_name":"Hood, Brad","first_name":"Brad","last_name":"Hood"},{"full_name":"Holota, Wolfgang","last_name":"Holota","first_name":"Wolfgang"},{"full_name":"Howe, Scott","last_name":"Howe","first_name":"Scott"},{"full_name":"Huang, Pei","first_name":"Pei","last_name":"Huang"},{"full_name":"Hull, Tony","first_name":"Tony","last_name":"Hull"},{"last_name":"Hunt","first_name":"Ron","full_name":"Hunt, Ron"},{"full_name":"Hurd, Kevin","first_name":"Kevin","last_name":"Hurd"},{"first_name":"Sandra","last_name":"Johnson","full_name":"Johnson, Sandra"},{"full_name":"Kissil, Andrew","first_name":"Andrew","last_name":"Kissil"},{"full_name":"Knight, Brent","last_name":"Knight","first_name":"Brent"},{"first_name":"Daniel","last_name":"Kolenz","full_name":"Kolenz, Daniel"},{"last_name":"Kraus","first_name":"Oliver","full_name":"Kraus, Oliver"},{"full_name":"Krist, John","first_name":"John","last_name":"Krist"},{"full_name":"Li, Mary","last_name":"Li","first_name":"Mary"},{"full_name":"Lisman, 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For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument."}],"extern":"1"},{"publication":"PLOS Computational Biology","citation":{"short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","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.","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.","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","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.","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","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402."},"article_type":"original","date_published":"2020-11-05T00:00:00Z","scopus_import":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"day":"05","article_processing_charge":"No","has_accepted_license":"1","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The Moran process on 2-chromatic graphs","ddc":["000"],"status":"public","intvolume":" 16","file":[{"date_created":"2020-11-18T07:26:10Z","date_updated":"2020-11-18T07:26:10Z","success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","file_id":"8768","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2498594,"file_name":"2020_PlosCompBio_Kaveh.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"11","external_id":{"isi":["000591317200004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1008402","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"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.","year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","author":[{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"last_name":"McAvoy","first_name":"Alex","full_name":"McAvoy, Alex"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"date_updated":"2023-08-22T12:49:18Z","date_created":"2020-11-18T07:20:23Z","volume":16,"article_number":"e1008402","file_date_updated":"2020-11-18T07:26:10Z"},{"type":"conference","abstract":[{"lang":"eng","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."}],"title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","status":"public","_id":"8750","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"04","citation":{"short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","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.","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.","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","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","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.","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."},"publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","date_published":"2020-12-04T00:00:00Z","article_number":"9314994","ec_funded":1,"publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2020","date_created":"2020-11-10T07:04:57Z","date_updated":"2023-08-22T12:48:18Z","author":[{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Freire, Daniel","first_name":"Daniel","last_name":"Freire"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"}],"publication_identifier":{"isbn":["9781728191485"]},"month":"12","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2006.12325"],"isi":["000661920400013"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.12325"}],"language":[{"iso":"eng"}],"doi":"10.1109/MEMOCODE51338.2020.9314994","conference":{"location":"Virtual Conference","start_date":"2020-12-02","end_date":"2020-12-04","name":"MEMOCODE: Conference on Formal Methods and Models for System Design"}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8758","intvolume":" 181","status":"public","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","ddc":["510"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9087","checksum":"bc2b63a90197b97cbc73eccada4639f5","success":1,"date_updated":"2021-02-04T10:29:11Z","date_created":"2021-02-04T10:29:11Z","access_level":"open_access","file_name":"2020_JourStatPhysics_Maas.pdf","file_size":753596,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","issue":"6","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."}],"citation":{"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","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.","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","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.","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."},"publication":"Journal of Statistical Physics","page":"2257-2303","article_type":"original","date_published":"2020-12-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","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).","year":"2020","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas"},{"full_name":"Mielke, Alexander","first_name":"Alexander","last_name":"Mielke"}],"volume":181,"date_created":"2020-11-15T23:01:18Z","date_updated":"2023-08-22T13:24:27Z","ec_funded":1,"file_date_updated":"2021-02-04T10:29:11Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000587107200002"],"arxiv":["2004.02831"]},"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s10955-020-02663-4","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"month":"12"},{"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"}],"type":"research_data_reference","date_created":"2023-05-23T16:42:30Z","date_updated":"2023-08-22T13:23:57Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea"},{"orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid"},{"full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8755"}]},"title":"Surpassing the resistance quantum with a geometric superinductor","ddc":["530"],"status":"public","publisher":"Zenodo","department":[{"_id":"JoFi"}],"year":"2020","_id":"13070","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","month":"09","article_processing_charge":"No","date_published":"2020-09-27T00:00:00Z","doi":"10.5281/ZENODO.4052882","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"oa":1,"citation":{"apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. 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