[{"external_id":{"arxiv":["1903.04046"]},"year":"2020","status":"public","publication":"Pure and Applied Analysis","date_published":"2020-01-01T00:00:00Z","publisher":"Mathematical Sciences Publishers","doi":"10.2140/paa.2020.2.35","article_processing_charge":"No","type":"journal_article","date_updated":"2024-01-29T09:01:12Z","_id":"14891","page":"35-73","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1903.04046","open_access":"1"}],"arxiv":1,"month":"01","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation in density functional theory,” <i>Pure and Applied Analysis</i>, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","ama":"Lewin M, Lieb EH, Seiringer R.  The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. 2020;2(1):35-73. doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2020).  The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>","mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>.","ista":"Lewin M, Lieb EH, Seiringer R. 2020.  The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2020. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>."},"oa_version":"Preprint","title":" The local density approximation in density functional theory","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Elliott H.","full_name":"Lieb, Elliott H.","last_name":"Lieb"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"scopus_import":"1","day":"01","article_type":"original","date_created":"2024-01-28T23:01:44Z","volume":2,"intvolume":"         2","abstract":[{"lang":"eng","text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"publication_status":"published"},{"pmid":1,"date_published":"2020-10-02T00:00:00Z","publication":"Journal of Molecular Biology","status":"public","keyword":["Molecular Biology","Structural Biology"],"year":"2020","external_id":{"pmid":["32910969"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"quality_controlled":"1","page":"5784-5801","date_updated":"2024-02-28T12:37:54Z","_id":"15036","type":"journal_article","doi":"10.1016/j.jmb.2020.09.001","article_processing_charge":"No","publisher":"Elsevier","issue":"21","citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"month":"10","publication_status":"published","publication_identifier":{"issn":["0022-2836"]},"abstract":[{"lang":"eng","text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed."}],"intvolume":"       432","volume":432,"article_type":"original","date_created":"2024-02-28T08:50:34Z","author":[{"last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias","first_name":"Higor Vinícius Dias"},{"full_name":"Leonardo, Diego Antonio","last_name":"Leonardo","first_name":"Diego Antonio"},{"first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel","last_name":"Brognara"},{"first_name":"José","full_name":"Brandão-Neto, José","last_name":"Brandão-Neto"},{"last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto","first_name":"Humberto"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"full_name":"Garratt, Richard Charles","last_name":"Garratt","first_name":"Richard Charles"}],"day":"02","oa_version":"Published Version","title":"Molecular recognition at septin interfaces: The switches hold the key"},{"page":"717-731","ddc":["580"],"quality_controlled":"1","doi":"10.1016/j.molp.2020.02.012","article_processing_charge":"No","publisher":"Elsevier","date_updated":"2024-02-28T12:41:52Z","_id":"15037","type":"journal_article","status":"public","publication":"Molecular Plant","pmid":1,"date_published":"2020-05-04T00:00:00Z","year":"2020","external_id":{"pmid":["32087370"]},"keyword":["Plant Science","Molecular Biology"],"has_accepted_license":"1","intvolume":"        13","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"publication_identifier":{"issn":["1674-2052"]},"publication_status":"published","file_date_updated":"2024-02-28T12:39:56Z","author":[{"full_name":"Moulinier-Anzola, Jeanette","last_name":"Moulinier-Anzola","first_name":"Jeanette"},{"first_name":"Maximilian","full_name":"Schwihla, Maximilian","last_name":"Schwihla"},{"full_name":"De-Araújo, Lucinda","last_name":"De-Araújo","first_name":"Lucinda"},{"first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina","last_name":"Artner"},{"first_name":"Lisa","full_name":"Jörg, Lisa","last_name":"Jörg"},{"first_name":"Nataliia","full_name":"Konstantinova, Nataliia","last_name":"Konstantinova"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"full_name":"Korbei, Barbara","last_name":"Korbei","first_name":"Barbara"}],"day":"04","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","oa_version":"Published Version","volume":13,"article_type":"original","date_created":"2024-02-28T08:55:56Z","oa":1,"language":[{"iso":"eng"}],"issue":"5","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. <i>Molecular Plant</i>. 2020;13(5):717-731. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>","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 <i>et al.</i>, “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” <i>Molecular Plant</i>, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","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.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>.","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.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>.","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. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","department":[{"_id":"EvBe"}],"file":[{"file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c538a5008f7827f62d17d40a3bfabe65","file_size":3089212,"date_created":"2024-02-28T12:39:56Z","creator":"dernst","date_updated":"2024-02-28T12:39:56Z","file_id":"15038"}]},{"keyword":["General Medicine"],"external_id":{"arxiv":["2002.12086"]},"year":"2020","conference":{"start_date":"2020-02-07","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence","location":"New York, NY, United States"},"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.","date_published":"2020-04-03T00:00:00Z","project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","status":"public","type":"journal_article","date_updated":"2024-03-04T08:30:16Z","_id":"15055","publisher":"Association for the Advancement of Artificial Intelligence","doi":"10.1609/aaai.v34i06.6531","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2002.12086"}],"page":"9794-9801","department":[{"_id":"KrCh"}],"month":"04","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"06","citation":{"apa":"Brázdil, T., Chatterjee, K., Novotný, P., &#38; Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. New York, NY, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">https://doi.org/10.1609/aaai.v34i06.6531</a>","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:<a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">10.1609/aaai.v34i06.6531</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. Association for the Advancement of Artificial Intelligence, 2020. <a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">https://doi.org/10.1609/aaai.v34i06.6531</a>.","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.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. 2020;34(06):9794-9801. doi:<a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">10.1609/aaai.v34i06.6531</a>"},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2024-03-04T08:07:22Z","volume":34,"title":"Reinforcement learning of risk-constrained policies in Markov decision processes","oa_version":"Preprint","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Petr","full_name":"Novotný, Petr","last_name":"Novotný"},{"first_name":"Jiří","last_name":"Vahala","full_name":"Vahala, Jiří"}],"day":"03","publication_status":"published","publication_identifier":{"issn":["2374-3468"]},"intvolume":"        34","abstract":[{"lang":"eng","text":"<jats:p>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.</jats:p>"}]},{"title":"VRK-1 extends life span by activation of AMPK via phosphorylation","oa_version":"Published Version","day":"01","author":[{"full_name":"Park, Sangsoon","last_name":"Park","first_name":"Sangsoon"},{"first_name":"Murat","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","last_name":"Artan"},{"first_name":"Seung Hyun","last_name":"Han","full_name":"Han, Seung Hyun"},{"first_name":"Hae-Eun H.","full_name":"Park, Hae-Eun H.","last_name":"Park"},{"last_name":"Jung","full_name":"Jung, Yoonji","first_name":"Yoonji"},{"first_name":"Ara B.","last_name":"Hwang","full_name":"Hwang, Ara B."},{"last_name":"Shin","full_name":"Shin, Won Sik","first_name":"Won Sik"},{"first_name":"Kyong-Tai","last_name":"Kim","full_name":"Kim, Kyong-Tai"},{"full_name":"Lee, Seung-Jae V.","last_name":"Lee","first_name":"Seung-Jae V."}],"date_created":"2024-03-04T09:41:57Z","article_type":"original","volume":6,"intvolume":"         6","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"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."}],"has_accepted_license":"1","file_date_updated":"2024-03-04T09:46:41Z","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","month":"07","file":[{"file_id":"15058","creator":"dernst","date_updated":"2024-03-04T09:46:41Z","file_size":1864415,"date_created":"2024-03-04T09:46:41Z","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2020_ScienceAdvances_Park.pdf","success":1}],"article_number":"aaw7824","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Park <i>et al.</i>, “VRK-1 extends life span by activation of AMPK via phosphorylation,” <i>Science Advances</i>, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","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).","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. <i>Science Advances</i>. 2020;6(27). doi:<a href=\"https://doi.org/10.1126/sciadv.aaw7824\">10.1126/sciadv.aaw7824</a>","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. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aaw7824\">https://doi.org/10.1126/sciadv.aaw7824</a>","mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” <i>Science Advances</i>, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.aaw7824\">10.1126/sciadv.aaw7824</a>.","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.” <i>Science Advances</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/sciadv.aaw7824\">https://doi.org/10.1126/sciadv.aaw7824</a>.","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."},"issue":"27","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","doi":"10.1126/sciadv.aaw7824","type":"journal_article","_id":"15057","date_updated":"2024-03-04T09:52:09Z","ddc":["570"],"quality_controlled":"1","year":"2020","publication":"Science Advances","status":"public","date_published":"2020-07-01T00:00:00Z","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":"08","article_processing_charge":"No","author":[{"last_name":"Wasiak","full_name":"Wasiak, Michal","first_name":"Michal"},{"full_name":"Botello, Gabriel Santamaria","last_name":"Botello","first_name":"Gabriel Santamaria"},{"last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos Atia","first_name":"Kerlos Atia"},{"last_name":"Sedlmeir","full_name":"Sedlmeir, Florian","first_name":"Florian"},{"last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R"},{"first_name":"Daniel","full_name":"Segovia-Vargas, Daniel","last_name":"Segovia-Vargas"},{"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"}],"doi":"10.23919/eucap48036.2020.9135962","title":"Compact millimeter and submillimeter-wave photonic radiometer for cubesats","oa_version":"None","publisher":"IEEE","_id":"15059","date_updated":"2024-03-04T10:02:49Z","date_created":"2024-03-04T09:57:48Z","type":"conference","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."}],"publication_identifier":{"eisbn":["9788831299008"]},"publication_status":"published","quality_controlled":"1","year":"2020","month":"07","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"publication":"14th European Conference on Antennas and Propagation","status":"public","citation":{"mla":"Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” <i>14th European Conference on Antennas and Propagation</i>, IEEE, 2020, doi:<a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">10.23919/eucap48036.2020.9135962</a>.","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 <i>14th European Conference on Antennas and Propagation</i>. Copenhagen, Denmark: IEEE. <a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">https://doi.org/10.23919/eucap48036.2020.9135962</a>","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 <i>14th European Conference on Antennas and Propagation</i>. IEEE, 2020. <a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">https://doi.org/10.23919/eucap48036.2020.9135962</a>.","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.","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.","ieee":"M. Wasiak <i>et al.</i>, “Compact millimeter and submillimeter-wave photonic radiometer for cubesats,” in <i>14th European Conference on Antennas and Propagation</i>, Copenhagen, Denmark, 2020.","ama":"Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In: <i>14th European Conference on Antennas and Propagation</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">10.23919/eucap48036.2020.9135962</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2020-03-20","start_date":"2020-03-15","name":"EuCAP: European Conference on Antennas and Propagation","location":"Copenhagen, Denmark"},"date_published":"2020-07-08T00:00:00Z","acknowledgement":"This work has been financially supported by Comunidad de Madrid S2018/NMT-4333 ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects."},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"}],"intvolume":"       117","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"}],"date_created":"2024-03-04T10:03:52Z","article_type":"original","volume":117,"title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","oa_version":"Published Version","day":"08","author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"full_name":"Zielinska, Karolina","last_name":"Zielinska","first_name":"Karolina"},{"last_name":"Babuta","full_name":"Babuta, Mrigya","first_name":"Mrigya"},{"first_name":"Joan L.","last_name":"Arolas","full_name":"Arolas, Joan L."},{"first_name":"Julius","last_name":"Kostan","full_name":"Kostan, Julius"},{"full_name":"Khan, Muhammad Bashir","last_name":"Khan","first_name":"Muhammad Bashir"},{"full_name":"Schreiner, Claudia","last_name":"Schreiner","first_name":"Claudia"},{"last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P","first_name":"Anita P"},{"full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli","first_name":"Luciano"},{"first_name":"Martin","full_name":"Puchinger, Martin","last_name":"Puchinger"},{"full_name":"Gkougkoulia, Eirini A.","last_name":"Gkougkoulia","first_name":"Eirini A."},{"last_name":"Ribeiro","full_name":"Ribeiro, Euripedes de Almeida","first_name":"Euripedes de Almeida"},{"full_name":"Marlovits, Thomas C.","last_name":"Marlovits","first_name":"Thomas C."},{"first_name":"Alok","full_name":"Bhattacharya, Alok","last_name":"Bhattacharya"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1917269117\">https://doi.org/10.1073/pnas.1917269117</a>.","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. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1917269117\">https://doi.org/10.1073/pnas.1917269117</a>","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:<a href=\"https://doi.org/10.1073/pnas.1917269117\">10.1073/pnas.1917269117</a>.","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. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(36):22101-22112. doi:<a href=\"https://doi.org/10.1073/pnas.1917269117\">10.1073/pnas.1917269117</a>","ieee":"N. Pinotsis <i>et al.</i>, “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","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."},"issue":"36","language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"CaBe"}],"month":"09","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.191726911","open_access":"1"}],"page":"22101-22112","type":"journal_article","_id":"15061","date_updated":"2024-03-04T10:14:44Z","publisher":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","doi":"10.1073/pnas.1917269117","date_published":"2020-09-08T00:00:00Z","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. ","pmid":1,"status":"public","publication":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["32848067"]},"year":"2020"},{"arxiv":1,"month":"11","department":[{"_id":"LaEr"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2020.1.101\">https://doi.org/10.2140/pmp.2020.1.101</a>","mla":"Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” <i>Probability and Mathematical Physics</i>, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:<a href=\"https://doi.org/10.2140/pmp.2020.1.101\">10.2140/pmp.2020.1.101</a>.","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.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2020. <a href=\"https://doi.org/10.2140/pmp.2020.1.101\">https://doi.org/10.2140/pmp.2020.1.101</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” <i>Probability and Mathematical Physics</i>, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146.","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. <i>Probability and Mathematical Physics</i>. 2020;1(1):101-146. doi:<a href=\"https://doi.org/10.2140/pmp.2020.1.101\">10.2140/pmp.2020.1.101</a>"},"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"16","author":[{"last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","first_name":"Giorgio"},{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Dominik J","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder"}],"title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","oa_version":"Preprint","volume":1,"date_created":"2024-03-04T10:27:57Z","article_type":"original","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"}],"intvolume":"         1","publication_identifier":{"issn":["2690-1005","2690-0998"]},"publication_status":"published","year":"2020","external_id":{"arxiv":["1908.01653"]},"keyword":["General Medicine"],"publication":"Probability and Mathematical Physics","status":"public","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"ec_funded":1,"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","date_published":"2020-11-16T00:00:00Z","article_processing_charge":"No","doi":"10.2140/pmp.2020.1.101","publisher":"Mathematical Sciences Publishers","_id":"15063","date_updated":"2024-03-04T10:33:15Z","type":"journal_article","page":"101-146","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1908.01653","open_access":"1"}],"quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” <i>Journal of Applied and Computational Topology</i>, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.","ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. <i>Journal of Applied and Computational Topology</i>. 2020;4(4):455-480. doi:<a href=\"https://doi.org/10.1007/s41468-020-00058-8\">10.1007/s41468-020-00058-8</a>","mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” <i>Journal of Applied and Computational Topology</i>, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:<a href=\"https://doi.org/10.1007/s41468-020-00058-8\">10.1007/s41468-020-00058-8</a>.","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-020-00058-8\">https://doi.org/10.1007/s41468-020-00058-8</a>","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s41468-020-00058-8\">https://doi.org/10.1007/s41468-020-00058-8</a>.","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."},"issue":"4","language":[{"iso":"eng"}],"oa":1,"file":[{"file_id":"15065","date_created":"2024-03-04T10:52:42Z","file_size":851190,"creator":"dernst","date_updated":"2024-03-04T10:52:42Z","relation":"main_file","checksum":"eed1168b6e66cd55272c19bb7fca8a1c","success":1,"file_name":"2020_JourApplCompTopology_Bauer.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"HeEd"}],"month":"12","file_date_updated":"2024-03-04T10:52:42Z","publication_status":"published","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"intvolume":"         4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"has_accepted_license":"1","date_created":"2024-03-04T10:47:49Z","article_type":"original","volume":4,"title":"Čech-Delaunay gradient flow and homology inference for self-maps","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"full_name":"Bauer, U.","last_name":"Bauer","first_name":"U."},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz","last_name":"Jablonski","orcid":"0000-0002-3536-9866","first_name":"Grzegorz"},{"full_name":"Mrozek, M.","last_name":"Mrozek","first_name":"M."}],"date_published":"2020-12-01T00:00:00Z","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":"Journal of Applied and Computational Topology","status":"public","year":"2020","quality_controlled":"1","ddc":["500"],"page":"455-480","type":"journal_article","_id":"15064","date_updated":"2024-03-04T10:54:04Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s41468-020-00058-8"},{"status":"public","publication":"34th International Symposium on Distributed Computing","date_published":"2020-10-07T00:00:00Z","conference":{"start_date":"2020-10-12","end_date":"2020-10-16","name":"DISC: Symposium on Distributed Computing","location":"Virtual"},"year":"2020","related_material":{"record":[{"id":"9678","status":"public","relation":"later_version"}]},"external_id":{"arxiv":["2005.07761"]},"ddc":["000"],"quality_controlled":"1","article_processing_charge":"No","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.DISC.2020.40","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"15074","date_updated":"2024-03-05T07:13:13Z","type":"conference","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: <i>34th International Symposium on Distributed Computing</i>. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">10.4230/LIPIcs.DISC.2020.40</a>","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in <i>34th International Symposium on Distributed Computing</i>, Virtual, 2020, vol. 179.","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.","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.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In <i>34th International Symposium on Distributed Computing</i>, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">https://doi.org/10.4230/LIPIcs.DISC.2020.40</a>.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., &#38; Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In <i>34th International Symposium on Distributed Computing</i> (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">https://doi.org/10.4230/LIPIcs.DISC.2020.40</a>","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” <i>34th International Symposium on Distributed Computing</i>, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">10.4230/LIPIcs.DISC.2020.40</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"month":"10","department":[{"_id":"DaAl"}],"article_number":"40","file":[{"file_id":"15075","date_created":"2024-03-05T07:08:27Z","file_size":303529,"date_updated":"2024-03-05T07:08:27Z","creator":"dernst","relation":"main_file","checksum":"23e2d9321aef53092dc1e24a8ab82d72","file_name":"2020_LIPIcs_Brandt.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/3.0/","abstract":[{"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.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)"},"intvolume":"       179","file_date_updated":"2024-03-05T07:08:27Z","publication_status":"published","day":"07","scopus_import":"1","author":[{"first_name":"Sebastian","last_name":"Brandt","full_name":"Brandt, Sebastian"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"},{"last_name":"Uitto","full_name":"Uitto, Jara","first_name":"Jara"}],"title":"Brief announcement: Efficient load-balancing through distributed token dropping","oa_version":"Published Version","volume":179,"date_created":"2024-03-05T07:09:12Z"},{"ddc":["000"],"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.ICALP.2020.7","alternative_title":["LIPIcs"],"article_processing_charge":"No","type":"conference","date_updated":"2024-03-05T07:35:53Z","_id":"15077","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication":"47th International Colloquium on Automata, Languages, and Programming","status":"public","date_published":"2020-06-29T00:00:00Z","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","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2020-07-08","end_date":"2020-07-11","location":"Saarbrücken, Germany, Virtual"},"ec_funded":1,"external_id":{"arxiv":["2003.09297"]},"related_material":{"record":[{"id":"8286","relation":"later_version","status":"public"}]},"year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)"},"intvolume":"       168","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","file_date_updated":"2024-03-05T07:25:15Z","title":"Dynamic averaging load balancing on cycles","oa_version":"Published Version","author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","orcid":"0000-0001-5634-0731"},{"first_name":"Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","full_name":"Sabour, Amirmojtaba","last_name":"Sabour"}],"day":"29","scopus_import":"1","date_created":"2024-03-05T07:25:37Z","volume":168,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In <i>47th International Colloquium on Automata, Languages, and Programming</i>, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2020.7\">https://doi.org/10.4230/LIPIcs.ICALP.2020.7</a>.","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.","apa":"Alistarh, D.-A., Nadiradze, G., &#38; Sabour, A. (2020). Dynamic averaging load balancing on cycles. In <i>47th International Colloquium on Automata, Languages, and Programming</i> (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2020.7\">https://doi.org/10.4230/LIPIcs.ICALP.2020.7</a>","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” <i>47th International Colloquium on Automata, Languages, and Programming</i>, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2020.7\">10.4230/LIPIcs.ICALP.2020.7</a>.","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: <i>47th International Colloquium on Automata, Languages, and Programming</i>. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2020.7\">10.4230/LIPIcs.ICALP.2020.7</a>","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in <i>47th International Colloquium on Automata, Languages, and Programming</i>, Saarbrücken, Germany, Virtual, 2020, vol. 168.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020."},"arxiv":1,"month":"06","article_number":"7","file":[{"file_id":"15078","creator":"dernst","date_updated":"2024-03-05T07:25:15Z","file_size":782987,"date_created":"2024-03-05T07:25:15Z","checksum":"e5eb16199f4ccfd77a321977eb3f026f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_LIPIcs_Alistarh.pdf"}],"department":[{"_id":"DaAl"}]},{"type":"conference","date_created":"2024-03-05T08:57:17Z","date_updated":"2024-03-05T09:00:07Z","_id":"15082","title":"Disjoint tree-compatible plane perfect matchings","oa_version":"Published Version","author":[{"first_name":"Oswin","last_name":"Aichholzer","full_name":"Aichholzer, Oswin"},{"first_name":"Julia","last_name":"Obmann","full_name":"Obmann, Julia"},{"last_name":"Patak","full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel"},{"last_name":"Perz","full_name":"Perz, Daniel","first_name":"Daniel"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec"}],"article_processing_charge":"No","day":"01","quality_controlled":"1","publication_status":"published","main_file_link":[{"url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf","open_access":"1"}],"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."}],"article_number":"56","department":[{"_id":"KrCh"},{"_id":"UlWa"}],"month":"04","year":"2020","conference":{"start_date":"2020-03-16","end_date":"2020-03-18","name":"EuroCG: European Workshop on Computational Geometry","location":"Würzburg, Germany, Virtual"},"date_published":"2020-04-01T00:00:00Z","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: <i>36th European Workshop on Computational Geometry</i>. ; 2020.","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 <i>36th European Workshop on Computational Geometry</i>, Würzburg, Germany, Virtual, 2020.","chicago":"Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In <i>36th European Workshop on Computational Geometry</i>, 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.","mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” <i>36th European Workshop on Computational Geometry</i>, 56, 2020.","apa":"Aichholzer, O., Obmann, J., Patak, P., Perz, D., &#38; Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In <i>36th European Workshop on Computational Geometry</i>. Würzburg, Germany, Virtual."},"language":[{"iso":"eng"}],"publication":"36th European Workshop on Computational Geometry","status":"public","oa":1},{"year":"2020","month":"07","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"department":[{"_id":"JoFi"}],"oa":1,"status":"public","citation":{"short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>","mla":"Arnold, Georg M., et al. <i>Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>.","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. <a href=\"https://doi.org/10.5281/ZENODO.3961561\">https://doi.org/10.5281/ZENODO.3961561</a>","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, <a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>.","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. <a href=\"https://doi.org/10.5281/ZENODO.3961561\">https://doi.org/10.5281/ZENODO.3961561</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-27T00:00:00Z","article_processing_charge":"No","day":"27","doi":"10.5281/ZENODO.3961561","author":[{"first_name":"Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"orcid":"0000-0001-6613-1378","first_name":"Matthias","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf"},{"orcid":"0000-0003-0415-1423","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R"},{"orcid":"0000-0001-9868-2166","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","last_name":"Hease"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"oa_version":"Published Version","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","publisher":"Zenodo","_id":"13056","date_updated":"2024-09-10T12:23:51Z","date_created":"2023-05-23T13:37:41Z","type":"research_data_reference","ddc":["530"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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."}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}]},{"oa_version":"Published Version","publisher":"Dryad","title":"Social immunity modulates competition between coinfecting pathogens","author":[{"last_name":"Milutinovic","full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara"},{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","first_name":"Miriam"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"doi":"10.5061/DRYAD.CRJDFN318","day":"19","article_processing_charge":"No","type":"research_data_reference","date_created":"2023-05-23T16:11:22Z","date_updated":"2023-09-05T16:04:48Z","_id":"13060","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","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."}],"ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.crjdfn318","open_access":"1"}],"related_material":{"record":[{"id":"7343","status":"public","relation":"used_in_publication"}]},"month":"12","year":"2020","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"status":"public","oa":1,"date_published":"2020-12-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Milutinovic, Barbara, et al. <i>Social Immunity Modulates Competition between Coinfecting Pathogens</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>.","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., &#38; Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">https://doi.org/10.5061/DRYAD.CRJDFN318</a>","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">https://doi.org/10.5061/DRYAD.CRJDFN318</a>.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>"}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"ddc":["570"],"date_updated":"2023-08-04T11:19:26Z","_id":"13065","type":"research_data_reference","date_created":"2023-05-23T16:30:20Z","doi":"10.5061/DRYAD.Q2BVQ83HD","author":[{"first_name":"Stephanie","full_name":"Arnoux, Stephanie","last_name":"Arnoux"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"day":"19","article_processing_charge":"No","publisher":"Dryad","title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","oa_version":"Published Version","citation":{"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, <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","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. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>","mla":"Arnoux, Stephanie, et al. <i>VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","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:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>","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.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020)."},"date_published":"2020-10-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","department":[{"_id":"NiBa"}],"year":"2020","related_material":{"record":[{"id":"8928","status":"public","relation":"used_in_publication"}],"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}]},"month":"10"},{"doi":"10.5281/ZENODO.4052882","author":[{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda"},{"first_name":"Andrea","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni"},{"orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"article_processing_charge":"No","day":"27","oa_version":"Published Version","publisher":"Zenodo","title":"Surpassing the resistance quantum with a geometric superinductor","date_updated":"2024-09-10T12:23:56Z","_id":"13070","type":"research_data_reference","date_created":"2023-05-23T16:42:30Z","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ddc":["530"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"year":"2020","related_material":{"record":[{"id":"8755","relation":"used_in_publication","status":"public"}]},"month":"09","department":[{"_id":"JoFi"}],"oa":1,"status":"public","citation":{"ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>.","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., &#38; Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>","mla":"Peruzzo, Matilda, et al. <i>Surpassing the Resistance Quantum with a Geometric Superinductor</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>."},"date_published":"2020-09-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","publisher":"Zenodo","oa_version":"Published Version","doi":"10.5281/ZENODO.4266025","author":[{"first_name":"William J","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease"},{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"},{"last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","first_name":"Rishabh"},{"last_name":"Wulf","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-6613-1378"},{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"day":"10","article_processing_charge":"No","type":"research_data_reference","date_created":"2023-05-23T16:44:11Z","date_updated":"2024-09-10T12:23:54Z","_id":"13071","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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."}],"ddc":["530"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"related_material":{"record":[{"id":"9114","relation":"used_in_publication","status":"public"}]},"month":"11","year":"2020","department":[{"_id":"JoFi"}],"status":"public","oa":1,"date_published":"2020-11-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>","mla":"Hease, William J., et al. <i>Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>","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. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>.","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, <a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>."}},{"department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8708"}]},"month":"09","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-22T00:00:00Z","citation":{"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:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","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. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","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, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>","mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>."},"status":"public","oa":1,"date_created":"2023-05-23T16:48:27Z","type":"research_data_reference","_id":"13073","date_updated":"2023-08-04T11:04:11Z","oa_version":"Published Version","publisher":"Dryad","title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","article_processing_charge":"No","day":"22","doi":"10.5061/DRYAD.R4XGXD29N","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"first_name":"Cathy","full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"last_name":"Welch","full_name":"Welch, John","first_name":"John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"ddc":["570"],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"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."}]},{"page":"i919-i927","main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1093/bioinformatics/btaa843","publisher":"Oxford University Press","_id":"14125","date_updated":"2023-09-11T10:21:00Z","type":"journal_article","publication":"Bioinformatics","status":"public","extern":"1","pmid":1,"date_published":"2020-12-01T00:00:00Z","year":"2020","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"external_id":{"pmid":["33381818"]},"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"abstract":[{"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.","lang":"eng"}],"intvolume":"        36","publication_status":"published","publication_identifier":{"eissn":["1367-4811"]},"day":"01","scopus_import":"1","author":[{"last_name":"Stark","full_name":"Stark, Stefan G","first_name":"Stefan G"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Ximena","full_name":"Bonilla, Ximena","last_name":"Bonilla"},{"first_name":"Stéphane","full_name":"Chevrier, Stéphane","last_name":"Chevrier"},{"full_name":"Singer, Franziska","last_name":"Singer","first_name":"Franziska"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"first_name":"Faisal S","full_name":"Al-Quaddoomi, Faisal S","last_name":"Al-Quaddoomi"},{"first_name":"Jonas","last_name":"Albinus","full_name":"Albinus, Jonas"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"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","full_name":"Bacac, Marina","last_name":"Bacac"},{"full_name":"Baumhoer, Daniel","last_name":"Baumhoer","first_name":"Daniel"},{"full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer","first_name":"Beatrice"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"last_name":"Beisel","full_name":"Beisel, 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Reinhard"},{"first_name":"Stefanie","full_name":"Engler, Stefanie","last_name":"Engler"},{"first_name":"Martin","last_name":"Erkens","full_name":"Erkens, Martin"},{"full_name":"Eschbach, Katja","last_name":"Eschbach","first_name":"Katja"},{"first_name":"Cinzia","full_name":"Esposito, Cinzia","last_name":"Esposito"},{"first_name":"André","full_name":"Fedier, André","last_name":"Fedier"},{"full_name":"Ferreira, Pedro","last_name":"Ferreira","first_name":"Pedro"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"first_name":"Anja L","last_name":"Frei","full_name":"Frei, Anja L"},{"last_name":"Frey","full_name":"Frey, Bruno","first_name":"Bruno"},{"last_name":"Goetze","full_name":"Goetze, Sandra","first_name":"Sandra"},{"full_name":"Grob, Linda","last_name":"Grob","first_name":"Linda"},{"first_name":"Gabriele","last_name":"Gut","full_name":"Gut, Gabriele"},{"first_name":"Detlef","full_name":"Günther, Detlef","last_name":"Günther"},{"last_name":"Haberecker","full_name":"Haberecker, Martina","first_name":"Martina"},{"first_name":"Pirmin","last_name":"Haeuptle","full_name":"Haeuptle, Pirmin"},{"first_name":"Viola","full_name":"Heinzelmann-Schwarz, Viola","last_name":"Heinzelmann-Schwarz"},{"full_name":"Herter, Sylvia","last_name":"Herter","first_name":"Sylvia"},{"first_name":"Rene","full_name":"Holtackers, Rene","last_name":"Holtackers"},{"last_name":"Huesser","full_name":"Huesser, Tamara","first_name":"Tamara"},{"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","full_name":"Jahn, Katharina","last_name":"Jahn"},{"last_name":"James","full_name":"James, Alva R","first_name":"Alva 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C","last_name":"Schwalie","first_name":"Petra C"},{"full_name":"Schwan, Severin","last_name":"Schwan","first_name":"Severin"},{"first_name":"Tobias","last_name":"Schär","full_name":"Schär, Tobias"},{"last_name":"Senti","full_name":"Senti, Gabriela","first_name":"Gabriela"},{"first_name":"Franziska","full_name":"Singer, Franziska","last_name":"Singer"},{"first_name":"Sujana","last_name":"Sivapatham","full_name":"Sivapatham, Sujana"},{"first_name":"Berend","last_name":"Snijder","full_name":"Snijder, Berend"},{"first_name":"Bettina","full_name":"Sobottka, Bettina","last_name":"Sobottka"},{"first_name":"Vipin T","full_name":"Sreedharan, Vipin T","last_name":"Sreedharan"},{"full_name":"Stark, Stefan","last_name":"Stark","first_name":"Stefan"},{"last_name":"Stekhoven","full_name":"Stekhoven, Daniel J","first_name":"Daniel J"},{"last_name":"Theocharides","full_name":"Theocharides, Alexandre PA","first_name":"Alexandre PA"},{"first_name":"Tinu M","full_name":"Thomas, Tinu M","last_name":"Thomas"},{"first_name":"Markus","full_name":"Tolnay, Markus","last_name":"Tolnay"},{"full_name":"Tosevski, Vinko","last_name":"Tosevski","first_name":"Vinko"},{"first_name":"Nora C","full_name":"Toussaint, Nora C","last_name":"Toussaint"},{"first_name":"Mustafa A","full_name":"Tuncel, Mustafa A","last_name":"Tuncel"},{"first_name":"Marina","full_name":"Tusup, Marina","last_name":"Tusup"},{"last_name":"Drogen","full_name":"Drogen, Audrey Van","first_name":"Audrey Van"},{"first_name":"Marcus","last_name":"Vetter","full_name":"Vetter, Marcus"},{"first_name":"Tatjana","last_name":"Vlajnic","full_name":"Vlajnic, Tatjana"},{"first_name":"Sandra","full_name":"Weber, Sandra","last_name":"Weber"},{"last_name":"Weber","full_name":"Weber, Walter P","first_name":"Walter P"},{"last_name":"Wegmann","full_name":"Wegmann, Rebekka","first_name":"Rebekka"},{"full_name":"Weller, Michael","last_name":"Weller","first_name":"Michael"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"full_name":"Wey, Norbert","last_name":"Wey","first_name":"Norbert"},{"first_name":"Andreas","full_name":"Wicki, Andreas","last_name":"Wicki"},{"first_name":"Bernd","last_name":"Wollscheid","full_name":"Wollscheid, Bernd"},{"first_name":"Shuqing","last_name":"Yu","full_name":"Yu, 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"},{"first_name":"Gregor","full_name":"Zuend, Gregor","last_name":"Zuend"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van","last_name":"Lehmann"}],"title":"SCIM: Universal single-cell matching with unpaired feature sets","oa_version":"Published Version","volume":36,"date_created":"2023-08-21T12:28:20Z","article_type":"original","oa":1,"language":[{"iso":"eng"}],"citation":{"ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","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.","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>","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. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","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.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>."},"issue":"Supplement_2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"FrLo"}]},{"date_created":"2023-08-22T14:07:26Z","volume":34,"title":"A commentary on the unsupervised learning of disentangled representations","oa_version":"Preprint","day":"28","scopus_import":"1","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"first_name":"Mario","full_name":"Lucic, Mario","last_name":"Lucic"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"publication_status":"published","publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"]},"intvolume":"        34","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."}],"department":[{"_id":"FrLo"}],"arxiv":1,"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” <i>The 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In <i>The 34th AAAI Conference on Artificial Intelligence</i> (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>","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 <i>The 34th AAAI Conference on Artificial Intelligence</i>, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>.","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.","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.","ieee":"F. Locatello <i>et al.</i>, “A commentary on the unsupervised learning of disentangled representations,” in <i>The 34th AAAI Conference on Artificial Intelligence</i>, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: <i>The 34th AAAI Conference on Artificial Intelligence</i>. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>"},"issue":"9","language":[{"iso":"eng"}],"oa":1,"type":"conference","_id":"14186","date_updated":"2023-09-12T07:44:48Z","publisher":"Association for the Advancement of Artificial Intelligence","article_processing_charge":"No","doi":"10.1609/aaai.v34i09.7120","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"page":"13681-13684","external_id":{"arxiv":["2007.14184"]},"year":"2020","date_published":"2020-07-28T00:00:00Z","conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2020-02-12","start_date":"2020-02-07","location":"New York, NY, United States"},"status":"public","extern":"1","publication":"The 34th AAAI Conference on Artificial Intelligence"}]