[{"publication_status":"published","status":"public","publication_identifier":{"issn":["1674-2052"]},"doi":"10.1016/j.molp.2020.02.012","abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"issue":"5","_id":"15037","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","author":[{"last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette"},{"first_name":"Maximilian","full_name":"Schwihla, Maximilian","last_name":"Schwihla"},{"last_name":"De-Araújo","full_name":"De-Araújo, Lucinda","first_name":"Lucinda"},{"first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","full_name":"Artner, Christina"},{"first_name":"Lisa","last_name":"Jörg","full_name":"Jörg, Lisa"},{"last_name":"Konstantinova","full_name":"Konstantinova, Nataliia","first_name":"Nataliia"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"first_name":"Barbara","full_name":"Korbei, Barbara","last_name":"Korbei"}],"article_processing_charge":"No","volume":13,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","relation":"main_file","creator":"dernst","file_size":3089212,"access_level":"open_access","content_type":"application/pdf","checksum":"c538a5008f7827f62d17d40a3bfabe65","success":1,"date_updated":"2024-02-28T12:39:56Z","file_id":"15038","date_created":"2024-02-28T12:39:56Z"}],"oa_version":"Published Version","ddc":["580"],"file_date_updated":"2024-02-28T12:39:56Z","month":"05","pmid":1,"citation":{"ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012."},"day":"04","page":"717-731","article_type":"original","date_updated":"2024-02-28T12:41:52Z","publication":"Molecular Plant","keyword":["Plant Science","Molecular Biology"],"year":"2020","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Elsevier","intvolume":" 13","date_created":"2024-02-28T08:55:56Z","date_published":"2020-05-04T00:00:00Z","external_id":{"pmid":["32087370"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_created":"2024-03-04T08:07:22Z","date_published":"2020-04-03T00:00:00Z","external_id":{"arxiv":["2002.12086"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.12086","open_access":"1"}],"intvolume":" 34","publisher":"Association for the Advancement of Artificial Intelligence","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"keyword":["General Medicine"],"year":"2020","date_updated":"2024-03-04T08:30:16Z","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","article_type":"original","page":"9794-9801","month":"04","day":"03","citation":{"apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531."},"conference":{"start_date":"2020-02-07","location":"New York, NY, United States","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence"},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":34,"_id":"15055","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Novotný","full_name":"Novotný, Petr","first_name":"Petr"},{"full_name":"Vahala, Jiří","last_name":"Vahala","first_name":"Jiří"}],"title":"Reinforcement learning of risk-constrained policies in Markov decision processes","doi":"10.1609/aaai.v34i06.6531","issue":"06","abstract":[{"text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.","lang":"eng"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"publication_identifier":{"issn":["2374-3468"]},"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","publication_status":"published","status":"public"},{"author":[{"full_name":"Park, Sangsoon","last_name":"Park","first_name":"Sangsoon"},{"full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","orcid":"0000-0001-8945-6992"},{"last_name":"Han","full_name":"Han, Seung Hyun","first_name":"Seung Hyun"},{"full_name":"Park, Hae-Eun H.","last_name":"Park","first_name":"Hae-Eun H."},{"first_name":"Yoonji","last_name":"Jung","full_name":"Jung, Yoonji"},{"first_name":"Ara B.","last_name":"Hwang","full_name":"Hwang, Ara B."},{"full_name":"Shin, Won Sik","last_name":"Shin","first_name":"Won Sik"},{"first_name":"Kyong-Tai","full_name":"Kim, Kyong-Tai","last_name":"Kim"},{"first_name":"Seung-Jae V.","full_name":"Lee, Seung-Jae V.","last_name":"Lee"}],"title":"VRK-1 extends life span by activation of AMPK via phosphorylation","_id":"15057","issue":"27","abstract":[{"lang":"eng","text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans."}],"doi":"10.1126/sciadv.aaw7824","publication_identifier":{"eissn":["2375-2548"]},"status":"public","publication_status":"published","acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ","day":"01","citation":{"mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824","ieee":"S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824","short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).","ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824."},"month":"07","ddc":["570"],"file_date_updated":"2024-03-04T09:46:41Z","oa_version":"Published Version","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"file_id":"15058","date_created":"2024-03-04T09:46:41Z","file_name":"2020_ScienceAdvances_Park.pdf","file_size":1864415,"relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","content_type":"application/pdf","success":1,"date_updated":"2024-03-04T09:46:41Z"}],"has_accepted_license":"1","volume":6,"article_processing_charge":"No","oa":1,"year":"2020","publication":"Science Advances","date_updated":"2024-03-04T09:52:09Z","article_type":"original","article_number":"aaw7824","department":[{"_id":"MaDe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-01T00:00:00Z","date_created":"2024-03-04T09:41:57Z","intvolume":" 6","publisher":"American Association for the Advancement of Science","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}]},{"publisher":"IEEE","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","citation":{"short":"M. Wasiak, G.S. Botello, K.A. Abdalmalak, F. Sedlmeir, A.R. Rueda Sanchez, D. Segovia-Vargas, H.G.L. Schwefel, L.E.G. Munoz, in:, 14th European Conference on Antennas and Propagation, IEEE, 2020.","ama":"Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In: 14th European Conference on Antennas and Propagation. IEEE; 2020. doi:10.23919/eucap48036.2020.9135962","ista":"Wasiak M, Botello GS, Abdalmalak KA, Sedlmeir F, Rueda Sanchez AR, Segovia-Vargas D, Schwefel HGL, Munoz LEG. 2020. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. 14th European Conference on Antennas and Propagation. EuCAP: European Conference on Antennas and Propagation.","apa":"Wasiak, M., Botello, G. S., Abdalmalak, K. A., Sedlmeir, F., Rueda Sanchez, A. R., Segovia-Vargas, D., … Munoz, L. E. G. (2020). Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In 14th European Conference on Antennas and Propagation. Copenhagen, Denmark: IEEE. https://doi.org/10.23919/eucap48036.2020.9135962","ieee":"M. Wasiak et al., “Compact millimeter and submillimeter-wave photonic radiometer for cubesats,” in 14th European Conference on Antennas and Propagation, Copenhagen, Denmark, 2020.","mla":"Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” 14th European Conference on Antennas and Propagation, IEEE, 2020, doi:10.23919/eucap48036.2020.9135962.","chicago":"Wasiak, Michal, Gabriel Santamaria Botello, Kerlos Atia Abdalmalak, Florian Sedlmeir, Alfredo R Rueda Sanchez, Daniel Segovia-Vargas, Harald G. L. Schwefel, and Luis Enrique Garcia Munoz. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” In 14th European Conference on Antennas and Propagation. IEEE, 2020. https://doi.org/10.23919/eucap48036.2020.9135962."},"day":"08","department":[{"_id":"JoFi"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-08T00:00:00Z","date_created":"2024-03-04T09:57:48Z","oa_version":"None","conference":{"name":"EuCAP: European Conference on Antennas and Propagation","start_date":"2020-03-15","location":"Copenhagen, Denmark","end_date":"2020-03-20"},"publication_identifier":{"eisbn":["9788831299008"]},"publication":"14th European Conference on Antennas and Propagation","date_updated":"2024-03-04T10:02:49Z","acknowledgement":"This work has been financially supported by Comunidad de Madrid S2018/NMT-4333 ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects.","publication_status":"published","status":"public","title":"Compact millimeter and submillimeter-wave photonic radiometer for cubesats","author":[{"full_name":"Wasiak, Michal","last_name":"Wasiak","first_name":"Michal"},{"first_name":"Gabriel Santamaria","full_name":"Botello, Gabriel Santamaria","last_name":"Botello"},{"first_name":"Kerlos Atia","last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos Atia"},{"last_name":"Sedlmeir","full_name":"Sedlmeir, Florian","first_name":"Florian"},{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"full_name":"Segovia-Vargas, Daniel","last_name":"Segovia-Vargas","first_name":"Daniel"},{"first_name":"Harald G. L.","last_name":"Schwefel","full_name":"Schwefel, Harald G. L."},{"first_name":"Luis Enrique Garcia","last_name":"Munoz","full_name":"Munoz, Luis Enrique Garcia"}],"_id":"15059","abstract":[{"lang":"eng","text":"In this paper we present a room temperature radiometer that can eliminate the need of using cryostats in satellite payload reducing its weight and improving reliability. The proposed radiometer is based on an electro-optic upconverter that boosts up microwave photons energy by upconverting them into an optical domain what makes them immune to thermal noise even if operating at room temperature. The converter uses a high-quality factor whispering gallery\r\nmode (WGM) resonator providing naturally narrow bandwidth and therefore might be useful for applications like microwave hyperspectral sensing. The upconversion process is explained by\r\nproviding essential information about photon conversion efficiency and sensitivity. To prove the concept, we describe an experiment which shows state-of-the-art photon conversion efficiency n=10-5 per mW of pump power at the frequency of 80 GHz."}],"year":"2020","doi":"10.23919/eucap48036.2020.9135962"},{"volume":117,"article_processing_charge":"No","citation":{"chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020."},"day":"08","month":"09","pmid":1,"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","status":"public","acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"first_name":"Karolina","full_name":"Zielinska, Karolina","last_name":"Zielinska"},{"full_name":"Babuta, Mrigya","last_name":"Babuta","first_name":"Mrigya"},{"first_name":"Joan L.","full_name":"Arolas, Joan L.","last_name":"Arolas"},{"full_name":"Kostan, Julius","last_name":"Kostan","first_name":"Julius"},{"first_name":"Muhammad Bashir","full_name":"Khan, Muhammad Bashir","last_name":"Khan"},{"first_name":"Claudia","full_name":"Schreiner, Claudia","last_name":"Schreiner"},{"last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luciano","last_name":"Ciccarelli","full_name":"Ciccarelli, Luciano"},{"first_name":"Martin","last_name":"Puchinger","full_name":"Puchinger, Martin"},{"last_name":"Gkougkoulia","full_name":"Gkougkoulia, Eirini A.","first_name":"Eirini A."},{"last_name":"Ribeiro","full_name":"Ribeiro, Euripedes de Almeida","first_name":"Euripedes de Almeida"},{"last_name":"Marlovits","full_name":"Marlovits, Thomas C.","first_name":"Thomas C."},{"last_name":"Bhattacharya","full_name":"Bhattacharya, Alok","first_name":"Alok"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"}],"_id":"15061","abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}],"issue":"36","doi":"10.1073/pnas.1917269117","publisher":"Proceedings of the National Academy of Sciences","main_file_link":[{"url":"https://doi.org/10.1073/pnas.191726911","open_access":"1"}],"intvolume":" 117","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"CaBe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-08T00:00:00Z","external_id":{"pmid":["32848067"]},"date_created":"2024-03-04T10:03:52Z","acknowledged_ssus":[{"_id":"LifeSc"}],"publication":"Proceedings of the National Academy of Sciences","date_updated":"2024-03-04T10:14:44Z","page":"22101-22112","article_type":"original","oa":1,"year":"2020"},{"volume":1,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","day":"16","citation":{"mla":"Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” Probability and Mathematical Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 2020;1(1):101-146. doi:10.2140/pmp.2020.1.101","ista":"Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 1(1), 101–146.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146."},"month":"11","acknowledgement":"Partially supported by ERC Advanced Grant No. 338804. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 66538","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2690-1005","2690-0998"]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"issue":"1","abstract":[{"text":"We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).","lang":"eng"}],"doi":"10.2140/pmp.2020.1.101","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"}],"title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","_id":"15063","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"intvolume":" 1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1908.01653"}],"publisher":"Mathematical Sciences Publishers","date_published":"2020-11-16T00:00:00Z","external_id":{"arxiv":["1908.01653"]},"scopus_import":"1","date_created":"2024-03-04T10:27:57Z","department":[{"_id":"LaEr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","page":"101-146","publication":"Probability and Mathematical Physics","date_updated":"2024-03-04T10:33:15Z","year":"2020","keyword":["General Medicine"],"oa":1},{"oa":1,"year":"2020","publication":"Journal of Applied and Computational Topology","date_updated":"2024-03-04T10:54:04Z","article_type":"original","page":"455-480","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-12-01T00:00:00Z","scopus_import":"1","date_created":"2024-03-04T10:47:49Z","intvolume":" 4","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","author":[{"last_name":"Bauer","full_name":"Bauer, U.","first_name":"U."},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"orcid":"0000-0002-3536-9866","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","full_name":"Jablonski, Grzegorz"},{"first_name":"M.","full_name":"Mrozek, M.","last_name":"Mrozek"}],"title":"Čech-Delaunay gradient flow and homology inference for self-maps","_id":"15064","issue":"4","abstract":[{"text":"We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.","lang":"eng"}],"doi":"10.1007/s41468-020-00058-8","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"status":"public","acknowledgement":"This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL.","publication_status":"published","day":"01","citation":{"mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8.","ista":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480.","ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020."},"ddc":["500"],"month":"12","file_date_updated":"2024-03-04T10:52:42Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":851190,"file_name":"2020_JourApplCompTopology_Bauer.pdf","date_updated":"2024-03-04T10:52:42Z","success":1,"checksum":"eed1168b6e66cd55272c19bb7fca8a1c","content_type":"application/pdf","access_level":"open_access","date_created":"2024-03-04T10:52:42Z","file_id":"15065"}],"has_accepted_license":"1","volume":4,"article_processing_charge":"Yes (via OA deal)"},{"external_id":{"arxiv":["2005.07761"]},"date_published":"2020-10-07T00:00:00Z","scopus_import":"1","date_created":"2024-03-05T07:09:12Z","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","intvolume":" 179","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2020","alternative_title":["LIPIcs"],"oa":1,"related_material":{"record":[{"id":"9678","relation":"later_version","status":"public"}]},"article_number":"40","publication":"34th International Symposium on Distributed Computing","date_updated":"2024-03-05T07:13:13Z","conference":{"name":"DISC: Symposium on Distributed Computing","end_date":"2020-10-16","location":"Virtual","start_date":"2020-10-12"},"oa_version":"Published Version","day":"07","citation":{"ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40."},"month":"10","file_date_updated":"2024-03-05T07:08:27Z","ddc":["000"],"has_accepted_license":"1","article_processing_charge":"No","volume":179,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"arxiv":1,"file":[{"date_updated":"2024-03-05T07:08:27Z","success":1,"content_type":"application/pdf","checksum":"23e2d9321aef53092dc1e24a8ab82d72","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":303529,"file_name":"2020_LIPIcs_Brandt.pdf","date_created":"2024-03-05T07:08:27Z","file_id":"15075"}],"abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds."}],"doi":"10.4230/LIPIcs.DISC.2020.40","author":[{"first_name":"Sebastian","last_name":"Brandt","full_name":"Brandt, Sebastian"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"full_name":"Suomela, Jukka","last_name":"Suomela","first_name":"Jukka"},{"first_name":"Jara","full_name":"Uitto, Jara","last_name":"Uitto"}],"title":"Brief announcement: Efficient load-balancing through distributed token dropping","_id":"15074","status":"public","publication_status":"published"},{"has_accepted_license":"1","volume":168,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"file":[{"file_name":"2020_LIPIcs_Alistarh.pdf","relation":"main_file","creator":"dernst","file_size":782987,"access_level":"open_access","content_type":"application/pdf","checksum":"e5eb16199f4ccfd77a321977eb3f026f","success":1,"date_updated":"2024-03-05T07:25:15Z","file_id":"15078","date_created":"2024-03-05T07:25:15Z"}],"arxiv":1,"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2020-07-11","location":"Saarbrücken, Germany, Virtual","start_date":"2020-07-08"},"oa_version":"Published Version","day":"29","citation":{"ista":"Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing on cycles. 47th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 168, 7.","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: 47th International Colloquium on Automata, Languages, and Programming. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging load balancing on cycles. In 47th International Colloquium on Automata, Languages, and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in 47th International Colloquium on Automata, Languages, and Programming, Saarbrücken, Germany, Virtual, 2020, vol. 168.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata, Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” 47th International Colloquium on Automata, Languages, and Programming, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7."},"month":"06","file_date_updated":"2024-03-05T07:25:15Z","ddc":["000"],"publication_status":"published","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier\r\nversions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments.\r\nFunding: European Research Council funding award PR1042ERC01","status":"public","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor."}],"doi":"10.4230/LIPIcs.ICALP.2020.7","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"full_name":"Sabour, Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba"}],"title":"Dynamic averaging load balancing on cycles","_id":"15077","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"intvolume":" 168","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["2003.09297"]},"date_published":"2020-06-29T00:00:00Z","scopus_import":"1","date_created":"2024-03-05T07:25:37Z","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"8286","relation":"later_version","status":"public"}]},"article_number":"7","publication":"47th International Colloquium on Automata, Languages, and Programming","date_updated":"2024-03-05T07:35:53Z","year":"2020","alternative_title":["LIPIcs"],"oa":1},{"publication":"36th European Workshop on Computational Geometry","date_updated":"2024-03-05T09:00:07Z","publication_status":"published","acknowledgement":"Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week, both held near Strobl, Austria. We are grateful to the participants for the inspiring atmosphere. We especially thank Alexander Pilz for bringing this class of problems to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734922.","status":"public","article_number":"56","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"last_name":"Obmann","full_name":"Obmann, Julia","first_name":"Julia"},{"full_name":"Patak, Pavel","last_name":"Patak","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel"},{"last_name":"Perz","full_name":"Perz, Daniel","first_name":"Daniel"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684"}],"title":"Disjoint tree-compatible plane perfect matchings","oa":1,"_id":"15082","year":"2020","abstract":[{"lang":"eng","text":"Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5, independent of n."}],"main_file_link":[{"open_access":"1","url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"KrCh"},{"_id":"UlWa"}],"day":"01","citation":{"ama":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: 36th European Workshop on Computational Geometry. ; 2020.","ista":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 56.","short":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020.","ieee":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible plane perfect matchings,” in 36th European Workshop on Computational Geometry, Würzburg, Germany, Virtual, 2020.","apa":"Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In 36th European Workshop on Computational Geometry. Würzburg, Germany, Virtual.","mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 2020.","chicago":"Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop on Computational Geometry, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","date_published":"2020-04-01T00:00:00Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","location":"Würzburg, Germany, Virtual","start_date":"2020-03-16","end_date":"2020-03-18"},"oa_version":"Published Version","date_created":"2024-03-05T08:57:17Z"},{"date_updated":"2024-09-10T12:23:51Z","related_material":{"record":[{"id":"8529","status":"public","relation":"used_in_publication"}]},"status":"public","_id":"13056","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","oa":1,"author":[{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","full_name":"Hease, William J","last_name":"Hease","orcid":"0000-0001-9868-2166"},{"orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"doi":"10.5281/ZENODO.3961561","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."}],"year":"2020","publisher":"Zenodo","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)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","type":"research_data_reference","month":"07","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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","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","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","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."},"department":[{"_id":"JoFi"}],"day":"27","date_created":"2023-05-23T13:37:41Z","oa_version":"Published Version","date_published":"2020-07-27T00:00:00Z"},{"type":"research_data_reference","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.crjdfn318","open_access":"1"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Dryad","date_published":"2020-12-19T00:00:00Z","date_created":"2023-05-23T16:11:22Z","oa_version":"Published Version","day":"19","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"citation":{"ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318."},"ddc":["570"],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"id":"7343","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-09-05T16:04:48Z","year":"2020","abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"doi":"10.5061/DRYAD.CRJDFN318","author":[{"orcid":"0000-0002-8214-4758","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","full_name":"Milutinovic, Barbara"},{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","full_name":"Stock, Miriam"},{"last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"oa":1,"title":"Social immunity modulates competition between coinfecting pathogens","_id":"13060"},{"oa_version":"Published Version","date_created":"2023-05-23T16:30:20Z","date_published":"2020-10-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"month":"10","citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD"},"day":"19","department":[{"_id":"NiBa"}],"article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"doi":"10.5061/DRYAD.Q2BVQ83HD","abstract":[{"lang":"eng","text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available."}],"year":"2020","_id":"13065","title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","oa":1,"author":[{"first_name":"Stephanie","last_name":"Arnoux","full_name":"Arnoux, Stephanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}],"record":[{"id":"8928","status":"public","relation":"used_in_publication"}]},"status":"public","date_updated":"2023-08-04T11:19:26Z"},{"type":"research_data_reference","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Zenodo","date_created":"2023-05-23T16:42:30Z","oa_version":"Published Version","date_published":"2020-09-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","ddc":["530"],"day":"27","department":[{"_id":"JoFi"}],"citation":{"apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882."},"status":"public","related_material":{"record":[{"id":"8755","relation":"used_in_publication","status":"public"}]},"date_updated":"2024-09-10T12:23:56Z","doi":"10.5281/ZENODO.4052882","year":"2020","abstract":[{"lang":"eng","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."}],"_id":"13070","author":[{"orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","full_name":"Peruzzo, Matilda"},{"full_name":"Trioni, Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea"},{"orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"}],"title":"Surpassing the resistance quantum with a geometric superinductor","oa":1},{"publisher":"Zenodo","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"article_processing_charge":"No","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","ddc":["530"],"citation":{"ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025","mla":"Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025."},"day":"10","department":[{"_id":"JoFi"}],"oa_version":"Published Version","date_created":"2023-05-23T16:44:11Z","date_published":"2020-11-10T00:00:00Z","date_updated":"2024-09-10T12:23:54Z","related_material":{"record":[{"id":"9114","relation":"used_in_publication","status":"public"}]},"status":"public","_id":"13071","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","oa":1,"author":[{"orcid":"0000-0001-9868-2166","last_name":"Hease","full_name":"Hease, William J","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sahu","full_name":"Sahu, Rishabh","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162"},{"last_name":"Wulf","full_name":"Wulf, Matthias","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378"},{"full_name":"Arnold, Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"doi":"10.5281/ZENODO.4266025","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request."}],"year":"2020"},{"related_material":{"record":[{"id":"8708","status":"public","relation":"used_in_publication"}]},"status":"public","date_updated":"2023-08-04T11:04:11Z","doi":"10.5061/DRYAD.R4XGXD29N","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"year":"2020","_id":"13073","title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","oa":1,"author":[{"first_name":"Alexis","full_name":"Simon, Alexis","last_name":"Simon"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"El Ayari","full_name":"El Ayari, Tahani","first_name":"Tahani"},{"first_name":"Cathy","last_name":"Liautard-Haag","full_name":"Liautard-Haag, Cathy"},{"last_name":"Strelkov","full_name":"Strelkov, Petr","first_name":"Petr"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","date_created":"2023-05-23T16:48:27Z","date_published":"2020-09-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","ddc":["570"],"citation":{"ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N."},"department":[{"_id":"NiBa"}],"day":"22"},{"intvolume":" 36","main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"publisher":"Oxford University Press","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"scopus_import":"1","date_created":"2023-08-21T12:28:20Z","date_published":"2020-12-01T00:00:00Z","external_id":{"pmid":["33381818"]},"extern":"1","date_updated":"2023-09-11T10:21:00Z","publication":"Bioinformatics","article_type":"original","page":"i919-i927","related_material":{"link":[{"relation":"software","url":"https://github.com/ratschlab/scim"}]},"oa":1,"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"year":"2020","volume":36,"article_processing_charge":"No","month":"12","pmid":1,"day":"01","citation":{"ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843."},"oa_version":"Published Version","publication_identifier":{"eissn":["1367-4811"]},"publication_status":"published","status":"public","_id":"14125","author":[{"last_name":"Stark","full_name":"Stark, Stefan G","first_name":"Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"first_name":"Ximena","full_name":"Bonilla, Ximena","last_name":"Bonilla"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"full_name":"Aebersold, Rudolf","last_name":"Aebersold","first_name":"Rudolf"},{"first_name":"Faisal S","last_name":"Al-Quaddoomi","full_name":"Al-Quaddoomi, Faisal S"},{"last_name":"Albinus","full_name":"Albinus, Jonas","first_name":"Jonas"},{"first_name":"Ilaria","full_name":"Alborelli, Ilaria","last_name":"Alborelli"},{"last_name":"Andani","full_name":"Andani, Sonali","first_name":"Sonali"},{"full_name":"Attinger, Per-Olof","last_name":"Attinger","first_name":"Per-Olof"},{"first_name":"Marina","last_name":"Bacac","full_name":"Bacac, Marina"},{"first_name":"Daniel","last_name":"Baumhoer","full_name":"Baumhoer, Daniel"},{"first_name":"Beatrice","last_name":"Beck-Schimmer","full_name":"Beck-Schimmer, Beatrice"},{"first_name":"Niko","full_name":"Beerenwinkel, Niko","last_name":"Beerenwinkel"},{"first_name":"Christian","last_name":"Beisel","full_name":"Beisel, Christian"},{"last_name":"Bernasconi","full_name":"Bernasconi, Lara","first_name":"Lara"},{"last_name":"Bertolini","full_name":"Bertolini, Anne","first_name":"Anne"},{"last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd","first_name":"Bernd"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"full_name":"Casanova, Ruben","last_name":"Casanova","first_name":"Ruben"},{"first_name":"Stéphane","full_name":"Chevrier, Stéphane","last_name":"Chevrier"},{"full_name":"Chicherova, Natalia","last_name":"Chicherova","first_name":"Natalia"},{"last_name":"D'Costa","full_name":"D'Costa, Maya","first_name":"Maya"},{"first_name":"Esther","last_name":"Danenberg","full_name":"Danenberg, Esther"},{"first_name":"Natalie","full_name":"Davidson, Natalie","last_name":"Davidson"},{"full_name":"gan, Monica-Andreea Dră","last_name":"gan","first_name":"Monica-Andreea Dră"},{"first_name":"Reinhard","last_name":"Dummer","full_name":"Dummer, Reinhard"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"full_name":"Erkens, Martin","last_name":"Erkens","first_name":"Martin"},{"first_name":"Katja","full_name":"Eschbach, Katja","last_name":"Eschbach"},{"last_name":"Esposito","full_name":"Esposito, Cinzia","first_name":"Cinzia"},{"full_name":"Fedier, André","last_name":"Fedier","first_name":"André"},{"first_name":"Pedro","last_name":"Ferreira","full_name":"Ferreira, Pedro"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"full_name":"Frei, Anja L","last_name":"Frei","first_name":"Anja L"},{"full_name":"Frey, Bruno","last_name":"Frey","first_name":"Bruno"},{"first_name":"Sandra","full_name":"Goetze, Sandra","last_name":"Goetze"},{"last_name":"Grob","full_name":"Grob, Linda","first_name":"Linda"},{"full_name":"Gut, Gabriele","last_name":"Gut","first_name":"Gabriele"},{"first_name":"Detlef","full_name":"Günther, Detlef","last_name":"Günther"},{"last_name":"Haberecker","full_name":"Haberecker, Martina","first_name":"Martina"},{"full_name":"Haeuptle, Pirmin","last_name":"Haeuptle","first_name":"Pirmin"},{"full_name":"Heinzelmann-Schwarz, Viola","last_name":"Heinzelmann-Schwarz","first_name":"Viola"},{"first_name":"Sylvia","full_name":"Herter, Sylvia","last_name":"Herter"},{"last_name":"Holtackers","full_name":"Holtackers, Rene","first_name":"Rene"},{"first_name":"Tamara","full_name":"Huesser, Tamara","last_name":"Huesser"},{"last_name":"Irmisch","full_name":"Irmisch, Anja","first_name":"Anja"},{"full_name":"Jacob, Francis","last_name":"Jacob","first_name":"Francis"},{"first_name":"Andrea","last_name":"Jacobs","full_name":"Jacobs, Andrea"},{"first_name":"Tim M","full_name":"Jaeger, Tim M","last_name":"Jaeger"},{"first_name":"Katharina","last_name":"Jahn","full_name":"Jahn, Katharina"},{"last_name":"James","full_name":"James, Alva R","first_name":"Alva R"},{"first_name":"Philip M","full_name":"Jermann, Philip M","last_name":"Jermann"},{"full_name":"Kahles, André","last_name":"Kahles","first_name":"André"},{"first_name":"Abdullah","last_name":"Kahraman","full_name":"Kahraman, Abdullah"},{"full_name":"Koelzer, Viktor H","last_name":"Koelzer","first_name":"Viktor H"},{"last_name":"Kuebler","full_name":"Kuebler, Werner","first_name":"Werner"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"full_name":"Kunze, Christian P","last_name":"Kunze","first_name":"Christian P"},{"first_name":"Christian","full_name":"Kurzeder, Christian","last_name":"Kurzeder"},{"last_name":"Lehmann","full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van"},{"last_name":"Levesque","full_name":"Levesque, Mitchell","first_name":"Mitchell"},{"full_name":"Lugert, Sebastian","last_name":"Lugert","first_name":"Sebastian"},{"first_name":"Gerd","full_name":"Maass, Gerd","last_name":"Maass"},{"first_name":"Markus","full_name":"Manz, Markus","last_name":"Manz"},{"full_name":"Markolin, Philipp","last_name":"Markolin","first_name":"Philipp"},{"first_name":"Julien","full_name":"Mena, Julien","last_name":"Mena"},{"last_name":"Menzel","full_name":"Menzel, Ulrike","first_name":"Ulrike"},{"last_name":"Metzler","full_name":"Metzler, Julian M","first_name":"Julian M"},{"first_name":"Nicola","last_name":"Miglino","full_name":"Miglino, Nicola"},{"full_name":"Milani, Emanuela S","last_name":"Milani","first_name":"Emanuela S"},{"first_name":"Holger","last_name":"Moch","full_name":"Moch, Holger"},{"full_name":"Muenst, Simone","last_name":"Muenst","first_name":"Simone"},{"first_name":"Riccardo","full_name":"Murri, Riccardo","last_name":"Murri"},{"first_name":"Charlotte KY","last_name":"Ng","full_name":"Ng, Charlotte KY"},{"first_name":"Stefan","full_name":"Nicolet, Stefan","last_name":"Nicolet"},{"last_name":"Nowak","full_name":"Nowak, Marta","first_name":"Marta"},{"last_name":"Pedrioli","full_name":"Pedrioli, Patrick GA","first_name":"Patrick GA"},{"full_name":"Pelkmans, Lucas","last_name":"Pelkmans","first_name":"Lucas"},{"last_name":"Piscuoglio","full_name":"Piscuoglio, Salvatore","first_name":"Salvatore"},{"last_name":"Prummer","full_name":"Prummer, Michael","first_name":"Michael"},{"first_name":"Mathilde","full_name":"Ritter, Mathilde","last_name":"Ritter"},{"first_name":"Christian","full_name":"Rommel, Christian","last_name":"Rommel"},{"last_name":"Rosano-González","full_name":"Rosano-González, María L","first_name":"María L"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Natascha","last_name":"Santacroce","full_name":"Santacroce, Natascha"},{"last_name":"Castillo","full_name":"Castillo, Jacobo Sarabia del","first_name":"Jacobo Sarabia del"},{"first_name":"Ramona","full_name":"Schlenker, Ramona","last_name":"Schlenker"},{"first_name":"Petra C","last_name":"Schwalie","full_name":"Schwalie, Petra C"},{"last_name":"Schwan","full_name":"Schwan, Severin","first_name":"Severin"},{"last_name":"Schär","full_name":"Schär, Tobias","first_name":"Tobias"},{"full_name":"Senti, Gabriela","last_name":"Senti","first_name":"Gabriela"},{"last_name":"Singer","full_name":"Singer, Franziska","first_name":"Franziska"},{"first_name":"Sujana","full_name":"Sivapatham, Sujana","last_name":"Sivapatham"},{"first_name":"Berend","last_name":"Snijder","full_name":"Snijder, Berend"},{"last_name":"Sobottka","full_name":"Sobottka, Bettina","first_name":"Bettina"},{"full_name":"Sreedharan, Vipin T","last_name":"Sreedharan","first_name":"Vipin T"},{"first_name":"Stefan","full_name":"Stark, Stefan","last_name":"Stark"},{"first_name":"Daniel J","full_name":"Stekhoven, Daniel J","last_name":"Stekhoven"},{"last_name":"Theocharides","full_name":"Theocharides, Alexandre PA","first_name":"Alexandre PA"},{"first_name":"Tinu M","full_name":"Thomas, Tinu M","last_name":"Thomas"},{"last_name":"Tolnay","full_name":"Tolnay, Markus","first_name":"Markus"},{"first_name":"Vinko","last_name":"Tosevski","full_name":"Tosevski, Vinko"},{"first_name":"Nora C","last_name":"Toussaint","full_name":"Toussaint, Nora C"},{"full_name":"Tuncel, Mustafa A","last_name":"Tuncel","first_name":"Mustafa A"},{"first_name":"Marina","last_name":"Tusup","full_name":"Tusup, Marina"},{"last_name":"Drogen","full_name":"Drogen, Audrey Van","first_name":"Audrey Van"},{"full_name":"Vetter, Marcus","last_name":"Vetter","first_name":"Marcus"},{"full_name":"Vlajnic, Tatjana","last_name":"Vlajnic","first_name":"Tatjana"},{"first_name":"Sandra","last_name":"Weber","full_name":"Weber, Sandra"},{"first_name":"Walter P","last_name":"Weber","full_name":"Weber, Walter P"},{"first_name":"Rebekka","last_name":"Wegmann","full_name":"Wegmann, Rebekka"},{"last_name":"Weller","full_name":"Weller, Michael","first_name":"Michael"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"first_name":"Norbert","last_name":"Wey","full_name":"Wey, Norbert"},{"last_name":"Wicki","full_name":"Wicki, Andreas","first_name":"Andreas"},{"last_name":"Wollscheid","full_name":"Wollscheid, Bernd","first_name":"Bernd"},{"full_name":"Yu, Shuqing","last_name":"Yu","first_name":"Shuqing"},{"last_name":"Ziegler","full_name":"Ziegler, Johanna","first_name":"Johanna"},{"first_name":"Marc","last_name":"Zimmermann","full_name":"Zimmermann, Marc"},{"first_name":"Martin","full_name":"Zoche, Martin","last_name":"Zoche"},{"full_name":"Zuend, Gregor","last_name":"Zuend","first_name":"Gregor"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Lehmann","full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van"}],"title":"SCIM: Universal single-cell matching with unpaired feature sets","doi":"10.1093/bioinformatics/btaa843","issue":"Supplement_2","abstract":[{"lang":"eng","text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively."}]},{"date_created":"2023-08-22T14:07:26Z","scopus_import":"1","external_id":{"arxiv":["2007.14184"]},"extern":"1","date_published":"2020-07-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","publisher":"Association for the Advancement of Artificial Intelligence","intvolume":" 34","main_file_link":[{"url":"https://arxiv.org/abs/2007.14184","open_access":"1"}],"year":"2020","oa":1,"page":"13681-13684","date_updated":"2023-09-12T07:44:48Z","publication":"The 34th AAAI Conference on Artificial Intelligence","oa_version":"Preprint","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"New York, NY, United States","start_date":"2020-02-07","end_date":"2020-02-12"},"month":"07","citation":{"ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120."},"day":"28","article_processing_charge":"No","volume":34,"arxiv":1,"doi":"10.1609/aaai.v34i09.7120","abstract":[{"lang":"eng","text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research."}],"issue":"9","_id":"14186","title":"A commentary on the unsupervised learning of disentangled representations","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Mario","full_name":"Lucic, Mario","last_name":"Lucic"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"status":"public","publication_status":"published","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"]}},{"abstract":[{"text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package.","lang":"eng"}],"title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","author":[{"first_name":"Geoffrey","last_name":"Négiar","full_name":"Négiar, Geoffrey"},{"first_name":"Gideon","last_name":"Dresdner","full_name":"Dresdner, Gideon"},{"first_name":"Alicia","full_name":"Tsai, Alicia","last_name":"Tsai"},{"full_name":"Ghaoui, Laurent El","last_name":"Ghaoui","first_name":"Laurent El"},{"orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Freund, Robert M.","last_name":"Freund","first_name":"Robert M."},{"first_name":"Fabian","last_name":"Pedregosa","full_name":"Pedregosa, Fabian"}],"_id":"14187","publication_status":"published","status":"public","oa_version":"Preprint","conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"citation":{"mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.","short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262."},"day":"27","month":"07","volume":119,"article_processing_charge":"No","arxiv":1,"year":"2020","alternative_title":["PMLR"],"oa":1,"page":"7253-7262","publication":"Proceedings of the 37th International Conference on Machine Learning","date_updated":"2023-09-12T08:03:40Z","external_id":{"arxiv":["2002.11860"]},"date_published":"2020-07-27T00:00:00Z","extern":"1","date_created":"2023-08-22T14:07:52Z","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2002.11860","open_access":"1"}],"intvolume":" 119"},{"day":"07","citation":{"chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359.","ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359."},"month":"07","conference":{"name":"International Conference on Machine Learning","location":"Virtual","start_date":"2020-07-13","end_date":"2020-07-18"},"oa_version":"Preprint","arxiv":1,"volume":119,"article_processing_charge":"No","author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Ben","full_name":"Poole, Ben","last_name":"Poole"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"}],"title":"Weakly-supervised disentanglement without compromises","_id":"14188","abstract":[{"lang":"eng","text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios."}],"status":"public","publication_status":"published","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2002.02886"]},"extern":"1","date_published":"2020-07-07T00:00:00Z","scopus_import":"1","date_created":"2023-08-22T14:08:14Z","main_file_link":[{"url":"https://arxiv.org/abs/2002.02886","open_access":"1"}],"intvolume":" 119","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","oa":1,"year":"2020","alternative_title":["PMLR"],"publication":"Proceedings of the 37th International Conference on Machine Learning","date_updated":"2023-09-12T07:59:29Z","page":"6348–6359"}]