[{"ec_funded":1,"file_date_updated":"2020-11-25T09:43:40Z","department":[{"_id":"GaNo"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N.","year":"2020","volume":43,"date_updated":"2023-08-21T08:25:31Z","date_created":"2020-06-14T22:00:49Z","author":[{"id":"D93538B0-5B71-11E9-AC62-02EBE5697425","last_name":"Parenti","first_name":"Ilaria","full_name":"Parenti, Ilaria"},{"last_name":"Garcia Rabaneda","first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E"},{"id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna","last_name":"Schön","full_name":"Schön, Hanna"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"publication_identifier":{"eissn":["1878108X"],"issn":["01662236"]},"month":"08","project":[{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32507511"],"isi":["000553090600008"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tins.2020.05.004","type":"journal_article","issue":"8","abstract":[{"text":"Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.","lang":"eng"}],"intvolume":" 43","title":"Neurodevelopmental disorders: From genetics to functional pathways","ddc":["570"],"status":"public","_id":"7957","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_TrendsNeuroscience_Parenti.pdf","creator":"dernst","content_type":"application/pdf","file_size":1439550,"file_id":"8805","relation":"main_file","success":1,"checksum":"67db0251b1d415ae59005f876fcf9e34","date_updated":"2020-11-25T09:43:40Z","date_created":"2020-11-25T09:43:40Z"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"608-621","article_type":"original","citation":{"mla":"Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:10.1016/j.tins.2020.05.004.","short":"I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621.","chicago":"Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.","ama":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621. doi:10.1016/j.tins.2020.05.004","ista":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.","ieee":"I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” Trends in Neurosciences, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.","apa":"Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004"},"publication":"Trends in Neurosciences","date_published":"2020-08-01T00:00:00Z"},{"_id":"7960","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 64","status":"public","title":"Intersection patterns of planar sets","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.","lang":"eng"}],"citation":{"ama":"Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z","apa":"Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z","ieee":"G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020.","ista":"Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete and Computational Geometry. 64, 304–323.","short":"G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323.","mla":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z.","chicago":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z."},"publication":"Discrete and Computational Geometry","page":"304-323","article_type":"original","date_published":"2020-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","year":"2020","acknowledgement":"We are very grateful to Pavel Paták for many helpful discussions and remarks. We also thank the referees for helpful comments, which greatly improved the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK was also partially supported by NSF grant DMS1300120. The research stay of ZP 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.","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"first_name":"Gil","last_name":"Kalai","full_name":"Kalai, Gil"},{"last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"}],"volume":64,"date_created":"2020-06-14T22:00:50Z","date_updated":"2023-08-21T08:26:34Z","oa":1,"external_id":{"arxiv":["1907.00885"],"isi":["000537329400001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.00885","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00454-020-00205-z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"09"},{"scopus_import":"1","day":"05","article_processing_charge":"No","publication":"Discrete and Computational Geometry","citation":{"chicago":"Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z.","short":"J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020) 888–917.","mla":"Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z.","apa":"Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00213-z","ieee":"J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection graphs of plane convex sets,” Discrete and Computational Geometry, vol. 63, no. 4. Springer Nature, pp. 888–917, 2020.","ista":"Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917.","ama":"Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917. doi:10.1007/s00454-020-00213-z"},"article_type":"original","page":"888-917","date_published":"2020-06-05T00:00:00Z","type":"journal_article","abstract":[{"text":"A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.","lang":"eng"}],"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7962","status":"public","title":"Almost all string graphs are intersection graphs of plane convex sets","intvolume":" 63","oa_version":"Preprint","month":"06","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"external_id":{"isi":["000538229000001"],"arxiv":["1803.06710"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.06710","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00454-020-00213-z","language":[{"iso":"eng"}],"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"author":[{"last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"},{"full_name":"Reed, Bruce","last_name":"Reed","first_name":"Bruce"},{"last_name":"Yuditsky","first_name":"Yelena","full_name":"Yuditsky, Yelena"}],"date_updated":"2023-08-21T08:49:18Z","date_created":"2020-06-14T22:00:51Z","volume":63},{"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2006.07382","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2006.07382"]},"language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/abbda5","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"11","publisher":"American Astronomical Society","publication_status":"published","year":"2020","volume":904,"date_updated":"2023-08-21T11:32:40Z","date_created":"2023-08-03T10:12:07Z","author":[{"full_name":"Götberg, Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","last_name":"Götberg"},{"first_name":"V.","last_name":"Korol","full_name":"Korol, V."},{"first_name":"A.","last_name":"Lamberts","full_name":"Lamberts, A."},{"last_name":"Kupfer","first_name":"T.","full_name":"Kupfer, T."},{"first_name":"K.","last_name":"Breivik","full_name":"Breivik, K."},{"full_name":"Ludwig, B.","last_name":"Ludwig","first_name":"B."},{"last_name":"Drout","first_name":"M. R.","full_name":"Drout, M. R."}],"article_number":"56","extern":"1","article_type":"original","citation":{"ama":"Götberg YLL, Korol V, Lamberts A, et al. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 2020;904(1). doi:10.3847/1538-4357/abbda5","ista":"Götberg YLL, Korol V, Lamberts A, Kupfer T, Breivik K, Ludwig B, Drout MR. 2020. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 904(1), 56.","apa":"Götberg, Y. L. L., Korol, V., Lamberts, A., Kupfer, T., Breivik, K., Ludwig, B., & Drout, M. R. (2020). Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abbda5","ieee":"Y. L. L. Götberg et al., “Stars stripped in binaries: The living gravitational-wave sources,” The Astrophysical Journal, vol. 904, no. 1. American Astronomical Society, 2020.","mla":"Götberg, Ylva Louise Linsdotter, et al. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal, vol. 904, no. 1, 56, American Astronomical Society, 2020, doi:10.3847/1538-4357/abbda5.","short":"Y.L.L. Götberg, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, M.R. Drout, The Astrophysical Journal 904 (2020).","chicago":"Götberg, Ylva Louise Linsdotter, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, and M. R. Drout. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal. American Astronomical Society, 2020. https://doi.org/10.3847/1538-4357/abbda5."},"publication":"The Astrophysical Journal","date_published":"2020-11-20T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","article_processing_charge":"No","day":"20","intvolume":" 904","title":"Stars stripped in binaries: The living gravitational-wave sources","status":"public","_id":"13460","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"Binary interaction can cause stellar envelopes to be stripped, which significantly reduces the radius of the star. The orbit of a binary composed of a stripped star and a compact object can therefore be so tight that the gravitational radiation the system produces reaches frequencies accessible to the Laser Interferometer Space Antenna (LISA). Two such stripped stars in tight orbits with white dwarfs are known so far (ZTF J2130+4420 and CD−30°11223), but many more are expected to exist. These binaries provide important constraints for binary evolution models and may be used as LISA verification sources. We develop a Monte Carlo code that uses detailed evolutionary models to simulate the Galactic population of stripped stars in tight orbits with either neutron star or white dwarf companions. We predict 0–100 stripped star + white dwarf binaries and 0–4 stripped star + neutron star binaries with a signal-to-noise ratio >5 after 10 yr of observations with LISA. More than 90% of these binaries are expected to show large radial velocity shifts of ≳200 $\\,\\mathrm{km}\\,{{\\rm{s}}}^{-1}$, which are spectroscopically detectable. Photometric variability due to tidal deformation of the stripped star is also expected and has been observed in ZTF J2130+4420 and CD−30°11223. In addition, the stripped star + neutron star binaries are expected to be X-ray bright with LX ≳ 1033–1036 $\\,\\mathrm{erg}\\,{{\\rm{s}}}^{-1}$. Our results show that stripped star binaries are promising multimessenger sources for the upcoming electromagnetic and gravitational wave facilities.","lang":"eng"}]},{"day":"08","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-06-08T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"chicago":"Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen, R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1.","short":"D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen, R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae, N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J. Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020).","mla":"Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature, 2020, doi:10.1038/s41467-020-16520-1.","ieee":"D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen, C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1","ista":"Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 11, 2865.","ama":"Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1"},"abstract":[{"text":"Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. ","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_NatureComm_Bayesian.pdf","creator":"dernst","file_size":1475657,"content_type":"application/pdf","file_id":"8000","relation":"main_file","checksum":"4c96babd4cfb0d153334f6c598c0bacb","date_created":"2020-06-22T11:24:32Z","date_updated":"2020-07-14T12:48:07Z"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Bayesian reassessment of the epigenetic architecture of complex traits","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7999","month":"06","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-16520-1","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32513961"],"isi":["000541702400004"]},"file_date_updated":"2020-07-14T12:48:07Z","article_number":"2865","date_created":"2020-06-22T11:18:25Z","date_updated":"2023-08-22T07:13:09Z","volume":11,"author":[{"full_name":"Trejo Banos, D","first_name":"D","last_name":"Trejo Banos"},{"full_name":"McCartney, DL","first_name":"DL","last_name":"McCartney"},{"last_name":"Patxot","first_name":"M","full_name":"Patxot, M"},{"first_name":"L","last_name":"Anchieri","full_name":"Anchieri, L"},{"full_name":"Battram, T","last_name":"Battram","first_name":"T"},{"full_name":"Christiansen, C","first_name":"C","last_name":"Christiansen"},{"full_name":"Costeira, R","first_name":"R","last_name":"Costeira"},{"first_name":"RM","last_name":"Walker","full_name":"Walker, RM"},{"full_name":"Morris, SW","first_name":"SW","last_name":"Morris"},{"last_name":"Campbell","first_name":"A","full_name":"Campbell, A"},{"full_name":"Zhang, Q","first_name":"Q","last_name":"Zhang"},{"full_name":"Porteous, DJ","first_name":"DJ","last_name":"Porteous"},{"last_name":"McRae","first_name":"AF","full_name":"McRae, AF"},{"full_name":"Wray, NR","first_name":"NR","last_name":"Wray"},{"last_name":"Visscher","first_name":"PM","full_name":"Visscher, PM"},{"full_name":"Haley, CS","last_name":"Haley","first_name":"CS"},{"full_name":"Evans, KL","last_name":"Evans","first_name":"KL"},{"first_name":"IJ","last_name":"Deary","full_name":"Deary, IJ"},{"last_name":"McIntosh","first_name":"AM","full_name":"McIntosh, AM"},{"full_name":"Hemani, G","first_name":"G","last_name":"Hemani"},{"full_name":"Bell, JT","last_name":"Bell","first_name":"JT"},{"first_name":"RE","last_name":"Marioni","full_name":"Marioni, RE"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19099-9","relation":"erratum"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"year":"2020","pmid":1},{"publication":"Evolution","citation":{"ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497.","short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027.","chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027."},"article_type":"original","page":"1482-1497","date_published":"2020-07-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7995","status":"public","title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","ddc":["570"],"intvolume":" 74","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_Evolution_Perini.pdf","creator":"dernst","file_size":1080810,"content_type":"application/pdf","file_id":"8808","relation":"main_file","success":1,"checksum":"56235bf1e2a9e25f96196bb13b6b754d","date_created":"2020-11-25T10:49:48Z","date_updated":"2020-11-25T10:49:48Z"}],"type":"journal_article","abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"issue":"7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000539780800001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"doi":"10.1111/evo.14027","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["15585646"],"issn":["00143820"]},"acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","year":"2020","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"id":"8809","status":"public","relation":"research_data"}]},"date_created":"2020-06-22T09:14:21Z","date_updated":"2023-08-22T07:13:38Z","volume":74,"file_date_updated":"2020-11-25T10:49:48Z","ec_funded":1},{"abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","related_material":{"record":[{"id":"7995","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"last_name":"Rafajlovic","first_name":"Marina","full_name":"Rafajlovic, Marina"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"oa_version":"Published Version","date_created":"2020-11-25T11:07:25Z","date_updated":"2023-08-22T07:13:37Z","year":"2020","_id":"8809","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"01","month":"07","doi":"10.5061/dryad.qrfj6q5cn","date_published":"2020-07-01T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.qrfj6q5cn","open_access":"1"}],"oa":1,"citation":{"mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020."}},{"page":"509-521","article_type":"original","citation":{"ama":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013","ista":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 107(3), 509–521.","apa":"Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.013","ieee":"D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3. Elsevier, pp. 509–521, 2020.","mla":"Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21, doi:10.1016/j.neuron.2020.05.013.","short":"D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020) 509–521.","chicago":"Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013."},"publication":"Neuron","date_published":"2020-08-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"05","intvolume":" 107","status":"public","ddc":["570"],"title":"Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8001","oa_version":"Published Version","file":[{"success":1,"checksum":"4030b2be0c9625d54694a1e9fb00305e","date_updated":"2020-11-25T11:23:02Z","date_created":"2020-11-25T11:23:02Z","file_id":"8811","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4390833,"access_level":"open_access","file_name":"2020_Neuron_Vandael.pdf"}],"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network."}],"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000556135600004"],"pmid":["32492366"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1016/j.neuron.2020.05.013","publication_identifier":{"issn":["0896-6273"],"eissn":["10974199"]},"month":"08","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung ( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs. Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian Marr for excellent technical assistance and cell reconstruction; Christina Altmutter for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of IST Austria for support.","year":"2020","volume":107,"date_created":"2020-06-22T13:29:05Z","date_updated":"2023-08-22T07:45:25Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/possible-physical-trace-of-short-term-memory-found/"}]},"author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H","full_name":"Vandael, David H"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina"},{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-11-25T11:23:02Z"},{"issue":"14","abstract":[{"text":"The interaction of strong near-infrared (NIR) laser pulses with wide-bandgap dielectrics produces high harmonics in the extreme ultraviolet (XUV) wavelength range. These observations have opened up the possibility of attosecond metrology in solids, which would benefit from a precise measurement of the emission times of individual harmonics with respect to the NIR laser field. Here we show that, when high-harmonics are detected from the input surface of a magnesium oxide crystal, a bichromatic probing of the XUV emission shows a clear synchronization largely consistent with a semiclassical model of electron–hole recollisions in bulk solids. On the other hand, the bichromatic spectrogram of harmonics originating from the exit surface of the 200 μm-thick crystal is strongly modified, indicating the influence of laser field distortions during propagation. Our tracking of sub-cycle electron and hole re-collisions at XUV energies is relevant to the development of solid-state sources of attosecond pulses.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13998","intvolume":" 53","status":"public","title":"Attosecond synchronization of extreme ultraviolet high harmonics from crystals","article_processing_charge":"No","day":"17","scopus_import":"1","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"date_published":"2020-06-17T00:00:00Z","citation":{"chicago":"Vampa, Giulio, Jian Lu, Yong Sing You, Denitsa Rangelova Baykusheva, Mengxi Wu, Hanzhe Liu, Kenneth J Schafer, Mette B Gaarde, David A Reis, and Shambhu Ghimire. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6455/ab8e56.","mla":"Vampa, Giulio, et al. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14, 144003, IOP Publishing, 2020, doi:10.1088/1361-6455/ab8e56.","short":"G. Vampa, J. Lu, Y.S. You, D.R. Baykusheva, M. Wu, H. Liu, K.J. Schafer, M.B. Gaarde, D.A. Reis, S. Ghimire, Journal of Physics B: Atomic, Molecular and Optical Physics 53 (2020).","ista":"Vampa G, Lu J, You YS, Baykusheva DR, Wu M, Liu H, Schafer KJ, Gaarde MB, Reis DA, Ghimire S. 2020. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 53(14), 144003.","apa":"Vampa, G., Lu, J., You, Y. S., Baykusheva, D. R., Wu, M., Liu, H., … Ghimire, S. (2020). Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/ab8e56","ieee":"G. Vampa et al., “Attosecond synchronization of extreme ultraviolet high harmonics from crystals,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14. IOP Publishing, 2020.","ama":"Vampa G, Lu J, You YS, et al. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 2020;53(14). doi:10.1088/1361-6455/ab8e56"},"publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","article_type":"original","extern":"1","article_number":"144003","author":[{"first_name":"Giulio","last_name":"Vampa","full_name":"Vampa, Giulio"},{"last_name":"Lu","first_name":"Jian","full_name":"Lu, Jian"},{"last_name":"You","first_name":"Yong Sing","full_name":"You, Yong Sing"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Wu","first_name":"Mengxi","full_name":"Wu, Mengxi"},{"first_name":"Hanzhe","last_name":"Liu","full_name":"Liu, Hanzhe"},{"first_name":"Kenneth J","last_name":"Schafer","full_name":"Schafer, Kenneth J"},{"full_name":"Gaarde, Mette B","first_name":"Mette B","last_name":"Gaarde"},{"full_name":"Reis, David A","first_name":"David A","last_name":"Reis"},{"first_name":"Shambhu","last_name":"Ghimire","full_name":"Ghimire, Shambhu"}],"volume":53,"date_created":"2023-08-09T13:09:51Z","date_updated":"2023-08-22T07:36:36Z","year":"2020","publisher":"IOP Publishing","publication_status":"published","publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"month":"06","doi":"10.1088/1361-6455/ab8e56","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2001.09951","open_access":"1"}],"external_id":{"arxiv":["2001.09951"]},"quality_controlled":"1"},{"day":"01","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"scopus_import":"1","date_published":"2020-07-01T00:00:00Z","article_type":"original","page":"778-783","publication":"Nature Physics","citation":{"ieee":"S. Biswas et al., “Probing molecular environment through photoemission delays,” Nature Physics, vol. 16, no. 7. Springer Nature, pp. 778–783, 2020.","apa":"Biswas, S., Förg, B., Ortmann, L., Schötz, J., Schweinberger, W., Zimmermann, T., … Kling, M. F. (2020). Probing molecular environment through photoemission delays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0887-8","ista":"Biswas S, Förg B, Ortmann L, Schötz J, Schweinberger W, Zimmermann T, Pi L, Baykusheva DR, Masood HA, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Hartmann G, Wörner HJ, Landsman AS, Kling MF. 2020. Probing molecular environment through photoemission delays. Nature Physics. 16(7), 778–783.","ama":"Biswas S, Förg B, Ortmann L, et al. Probing molecular environment through photoemission delays. Nature Physics. 2020;16(7):778-783. doi:10.1038/s41567-020-0887-8","chicago":"Biswas, Shubhadeep, Benjamin Förg, Lisa Ortmann, Johannes Schötz, Wolfgang Schweinberger, Tomáš Zimmermann, Liangwen Pi, et al. “Probing Molecular Environment through Photoemission Delays.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0887-8.","short":"S. Biswas, B. Förg, L. Ortmann, J. Schötz, W. Schweinberger, T. Zimmermann, L. Pi, D.R. Baykusheva, H.A. Masood, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, G. Hartmann, H.J. Wörner, A.S. Landsman, M.F. Kling, Nature Physics 16 (2020) 778–783.","mla":"Biswas, Shubhadeep, et al. “Probing Molecular Environment through Photoemission Delays.” Nature Physics, vol. 16, no. 7, Springer Nature, 2020, pp. 778–83, doi:10.1038/s41567-020-0887-8."},"abstract":[{"lang":"eng","text":"Attosecond chronoscopy has revealed small but measurable delays in photoionization, characterized by the ejection of an electron on absorption of a single photon. Ionization-delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect, resonances, electron correlations and transport. However, extending this approach to molecules presents challenges, such as identifying the correct ionization channels and the effect of the anisotropic molecular landscape on the measured delays. Here, we measure ionization delays from ethyl iodide around a giant dipole resonance. By using the theoretical value for the iodine atom as a reference, we disentangle the contribution from the functional ethyl group, which is responsible for the characteristic chemical reactivity of a molecule. We find a substantial additional delay caused by the presence of a functional group, which encodes the effect of the molecular potential on the departing electron. Such information is inaccessible to the conventional approach of measuring photoionization cross-sections. The results establish ionization-delay measurements as a valuable tool in investigating the electronic properties of molecules."}],"issue":"7","type":"journal_article","oa_version":"None","title":"Probing molecular environment through photoemission delays","status":"public","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13999","month":"07","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41567-020-0887-8","quality_controlled":"1","extern":"1","date_updated":"2023-08-22T07:38:04Z","date_created":"2023-08-09T13:10:07Z","volume":16,"author":[{"first_name":"Shubhadeep","last_name":"Biswas","full_name":"Biswas, Shubhadeep"},{"full_name":"Förg, Benjamin","first_name":"Benjamin","last_name":"Förg"},{"first_name":"Lisa","last_name":"Ortmann","full_name":"Ortmann, Lisa"},{"first_name":"Johannes","last_name":"Schötz","full_name":"Schötz, Johannes"},{"full_name":"Schweinberger, Wolfgang","first_name":"Wolfgang","last_name":"Schweinberger"},{"full_name":"Zimmermann, Tomáš","first_name":"Tomáš","last_name":"Zimmermann"},{"full_name":"Pi, Liangwen","last_name":"Pi","first_name":"Liangwen"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Masood","first_name":"Hafiz A.","full_name":"Masood, Hafiz A."},{"first_name":"Ioannis","last_name":"Liontos","full_name":"Liontos, Ioannis"},{"last_name":"Kamal","first_name":"Amgad M.","full_name":"Kamal, Amgad M."},{"last_name":"Kling","first_name":"Nora G.","full_name":"Kling, Nora G."},{"full_name":"Alharbi, Abdullah F.","first_name":"Abdullah F.","last_name":"Alharbi"},{"full_name":"Alharbi, Meshaal","last_name":"Alharbi","first_name":"Meshaal"},{"first_name":"Abdallah M.","last_name":"Azzeer","full_name":"Azzeer, Abdallah M."},{"full_name":"Hartmann, Gregor","first_name":"Gregor","last_name":"Hartmann"},{"full_name":"Wörner, Hans J.","first_name":"Hans J.","last_name":"Wörner"},{"first_name":"Alexandra S.","last_name":"Landsman","full_name":"Landsman, Alexandra S."},{"full_name":"Kling, Matthias F.","last_name":"Kling","first_name":"Matthias F."}],"publication_status":"published","publisher":"Springer Nature","year":"2020"},{"oa_version":"Published Version","file":[{"creator":"cziletti","file_size":2600967,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_QuantumSciTechnol_Fink.pdf","checksum":"8f25f05053f511f892ae8fa93f341e61","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-30T10:29:10Z","file_id":"8072","relation":"main_file"}],"_id":"8038","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator","ddc":["530"],"status":"public","intvolume":" 5","abstract":[{"text":"Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2020-05-25T00:00:00Z","publication":"Quantum Science and Technology","citation":{"ista":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 5(3), 034011.","apa":"Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020). Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab8dce","ieee":"J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing, 2020.","ama":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce","chicago":"Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab8dce.","mla":"Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce.","short":"J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and Technology 5 (2020)."},"article_type":"original","day":"25","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"first_name":"M.","last_name":"Kalaee","full_name":"Kalaee, M."},{"last_name":"Norte","first_name":"R.","full_name":"Norte, R."},{"last_name":"Pitanti","first_name":"A.","full_name":"Pitanti, A."},{"first_name":"O.","last_name":"Painter","full_name":"Painter, O."}],"date_created":"2020-06-29T07:59:35Z","date_updated":"2023-08-22T07:49:01Z","volume":5,"year":"2020","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","file_date_updated":"2020-07-14T12:48:08Z","ec_funded":1,"article_number":"034011","doi":"10.1088/2058-9565/ab8dce","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000539300800001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"month":"05","publication_identifier":{"eissn":["20589565"]}},{"date_published":"2020-06-19T00:00:00Z","citation":{"ista":"Lukacisinova M, Fernando B, Bollenbach MT. 2020. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 11, 3105.","ieee":"M. Lukacisinova, B. Fernando, and M. T. Bollenbach, “Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Lukacisinova, M., Fernando, B., & Bollenbach, M. T. (2020). Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16932-z","ama":"Lukacisinova M, Fernando B, Bollenbach MT. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-16932-z","chicago":"Lukacisinova, Marta, Booshini Fernando, and Mark Tobias Bollenbach. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16932-z.","mla":"Lukacisinova, Marta, et al. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications, vol. 11, 3105, Springer Nature, 2020, doi:10.1038/s41467-020-16932-z.","short":"M. Lukacisinova, B. Fernando, M.T. Bollenbach, Nature Communications 11 (2020)."},"publication":"Nature Communications","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","file":[{"file_id":"8071","relation":"main_file","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-30T09:58:50Z","checksum":"4f5f49d63add331d5eb8a2bae477b396","file_name":"2020_NatureComm_Lukacisinova.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":1546491}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8037","intvolume":" 11","status":"public","ddc":["570"],"title":"Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance","abstract":[{"lang":"eng","text":"Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics."}],"type":"journal_article","doi":"10.1038/s41467-020-16932-z","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000545685100002"],"pmid":["32561723"]},"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"month":"06","author":[{"full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fernando","first_name":"Booshini","full_name":"Fernando, Booshini"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"}],"volume":11,"date_updated":"2023-08-22T07:48:30Z","date_created":"2020-06-29T07:59:35Z","pmid":1,"year":"2020","publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:48:08Z","extern":"1","article_number":"3105"},{"article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2020-05-20T00:00:00Z","page":"9220-9230","article_type":"original","citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.","mla":"Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society, vol. 142, no. 20, American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142 (2020) 9220–9230.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 142(20), 9220–9230.","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I,” Journal of the American Chemical Society, vol. 142, no. 20. American Chemical Society, pp. 9220–9230, 2020.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b13450","ama":"Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230. doi:10.1021/jacs.9b13450"},"publication":"Journal of the American Chemical Society","issue":"20","abstract":[{"text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 142","title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8040","publication_identifier":{"issn":["00027863"],"eissn":["15205126"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1021/jacs.9b13450","isi":1,"quality_controlled":"1","external_id":{"pmid":["32347721"],"isi":["000537415600020"]},"volume":142,"date_updated":"2023-08-22T07:49:38Z","date_created":"2020-06-29T07:59:35Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9326"},{"id":"9713","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9878"}]},"author":[{"last_name":"Gupta","first_name":"Chitrak","full_name":"Gupta, Chitrak"},{"full_name":"Khaniya, Umesh","first_name":"Umesh","last_name":"Khaniya"},{"last_name":"Chan","first_name":"Chun Kit","full_name":"Chan, Chun Kit"},{"last_name":"Dehez","first_name":"Francois","full_name":"Dehez, Francois"},{"last_name":"Shekhar","first_name":"Mrinal","full_name":"Shekhar, Mrinal"},{"full_name":"Gunner, M. R.","last_name":"Gunner","first_name":"M. R."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"first_name":"Abhishek","last_name":"Singharoy","full_name":"Singharoy, Abhishek"}],"department":[{"_id":"LeSa"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2020"},{"type":"journal_article","abstract":[{"lang":"eng","text":"When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves."}],"ddc":["530"],"title":"Magnetically powered metachronal waves induce locomotion in self-assemblies","status":"public","intvolume":" 3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8036","oa_version":"Published Version","file":[{"file_name":"2020_CommunicationsPhysics_Collard.pdf","access_level":"open_access","file_size":1907821,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8045","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-29T13:21:24Z","checksum":"ed984f7a393f19140b5279a54a3336ad"}],"scopus_import":"1","day":"19","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Communications Physics","citation":{"short":"Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020).","mla":"Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature, 2020, doi:10.1038/s42005-020-0380-9.","chicago":"Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9.","ama":"Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9","ieee":"Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal waves induce locomotion in self-assemblies,” Communications Physics, vol. 3. Springer Nature, 2020.","apa":"Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-0380-9","ista":"Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 3, 112."},"date_published":"2020-06-19T00:00:00Z","article_number":"112","file_date_updated":"2020-07-14T12:48:08Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"Springer Nature","year":"2020","date_created":"2020-06-29T07:59:35Z","date_updated":"2023-08-22T07:47:30Z","volume":3,"author":[{"full_name":"Collard, Ylona","first_name":"Ylona","last_name":"Collard"},{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","first_name":"Galien M","last_name":"Grosjean","full_name":"Grosjean, Galien M"},{"full_name":"Vandewalle, Nicolas","last_name":"Vandewalle","first_name":"Nicolas"}],"month":"06","publication_identifier":{"eissn":["23993650"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000543328000002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42005-020-0380-9"},{"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2020.322","isi":1,"quality_controlled":"1","external_id":{"isi":["000539132300001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"month":"08","publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"date_updated":"2023-08-22T07:48:02Z","date_created":"2020-06-29T07:59:35Z","volume":897,"author":[{"full_name":"Paranjape, Chaitanya S","first_name":"Chaitanya S","last_name":"Paranjape","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yohann","last_name":"Duguet","full_name":"Duguet, Yohann"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"publication_status":"published","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"year":"2020","acknowledgement":"The authors thank S. Zammert and B. Budanur for useful discussions. J. F. Gibson is gratefully acknowledged for the development and the maintenance of the code Channelflow. Y.D. would like to thank P. Schlatter and D. S. Henningson for an early collaboration on a similar topic in the case of plane Couette flow during the years 2008–2013.","file_date_updated":"2020-07-14T12:48:08Z","article_number":"A7","date_published":"2020-08-25T00:00:00Z","article_type":"original","publication":"Journal of Fluid Mechanics","citation":{"ista":"Paranjape CS, Duguet Y, Hof B. 2020. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 897, A7.","ieee":"C. S. Paranjape, Y. Duguet, and B. Hof, “Oblique stripe solutions of channel flow,” Journal of Fluid Mechanics, vol. 897. Cambridge University Press, 2020.","apa":"Paranjape, C. S., Duguet, Y., & Hof, B. (2020). Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.322","ama":"Paranjape CS, Duguet Y, Hof B. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 2020;897. doi:10.1017/jfm.2020.322","chicago":"Paranjape, Chaitanya S, Yohann Duguet, and Björn Hof. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2020. https://doi.org/10.1017/jfm.2020.322.","mla":"Paranjape, Chaitanya S., et al. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics, vol. 897, A7, Cambridge University Press, 2020, doi:10.1017/jfm.2020.322.","short":"C.S. Paranjape, Y. Duguet, B. Hof, Journal of Fluid Mechanics 897 (2020)."},"day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","file":[{"date_created":"2020-06-30T08:37:37Z","date_updated":"2020-07-14T12:48:08Z","checksum":"3f487bf6d9286787096306eaa18702e8","file_id":"8070","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":767873,"file_name":"2020_JournalOfFluidMech_Paranjape.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["530"],"title":"Oblique stripe solutions of channel flow","intvolume":" 897","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8043","abstract":[{"lang":"eng","text":"With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain."}],"type":"journal_article"},{"month":"05","day":"20","article_processing_charge":"No","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002"},"main_file_link":[{"open_access":"1"}],"doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","type":"research_data_reference","license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.","lang":"eng"}],"status":"public","title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","publisher":"American Chemical Society","department":[{"_id":"LeSa"}],"_id":"9326","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","date_updated":"2023-08-22T07:49:37Z","date_created":"2021-04-14T12:05:20Z","oa_version":"Published Version","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"full_name":"Khaniya, Umesh","first_name":"Umesh","last_name":"Khaniya"},{"full_name":"Chan, Chun","first_name":"Chun","last_name":"Chan"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"full_name":"Shekhar, Mrinal","first_name":"Mrinal","last_name":"Shekhar"},{"last_name":"Gunner","first_name":"M. R.","full_name":"Gunner, M. R."},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"full_name":"Singharoy, Abhishek","first_name":"Abhishek","last_name":"Singharoy"}],"related_material":{"record":[{"id":"8040","status":"public","relation":"used_in_publication"}]}},{"author":[{"full_name":"Boccato, Chiara","first_name":"Chiara","last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brennecke, Christian","first_name":"Christian","last_name":"Brennecke"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"volume":22,"date_created":"2020-06-29T07:59:35Z","date_updated":"2023-08-22T07:47:04Z","year":"2020","department":[{"_id":"RoSe"}],"publisher":"European Mathematical Society","publication_status":"published","doi":"10.4171/JEMS/966","language":[{"iso":"eng"}],"external_id":{"arxiv":["1704.04819"],"isi":["000548174700006"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04819"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["14359855"]},"month":"07","oa_version":"Preprint","_id":"8042","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 22","title":"The excitation spectrum of Bose gases interacting through singular potentials","status":"public","issue":"7","abstract":[{"text":"We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.","lang":"eng"}],"type":"journal_article","date_published":"2020-07-01T00:00:00Z","citation":{"chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. European Mathematical Society, 2020. https://doi.org/10.4171/JEMS/966.","mla":"Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403, 2020.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966"},"publication":"Journal of the European Mathematical Society","page":"2331-2403","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"publisher":"American Chemical Society ","department":[{"_id":"LeSa"}],"title":"Supporting information","status":"public","_id":"9713","year":"2020","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-08-22T07:49:38Z","date_created":"2021-07-23T12:02:39Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8040"}]},"author":[{"full_name":"Gupta, Chitrak","last_name":"Gupta","first_name":"Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"last_name":"Chan","first_name":"Chun Kit","full_name":"Chan, Chun Kit"},{"full_name":"Dehez, Francois","first_name":"Francois","last_name":"Dehez"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"full_name":"Gunner, M.R.","last_name":"Gunner","first_name":"M.R."},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"last_name":"Singharoy","first_name":"Abhishek","full_name":"Singharoy, Abhishek"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Additional analyses of the trajectories"}],"citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001.","mla":"Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001","ieee":"C. Gupta et al., “Supporting information.” American Chemical Society , 2020.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001"},"doi":"10.1021/jacs.9b13450.s001","date_published":"2020-05-20T00:00:00Z","article_processing_charge":"No","month":"05","day":"20"},{"type":"research_data_reference","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"full_name":"Khaniya, Umesh","last_name":"Khaniya","first_name":"Umesh"},{"full_name":"Chan, Chun Kit","first_name":"Chun Kit","last_name":"Chan"},{"last_name":"Dehez","first_name":"Francois","full_name":"Dehez, Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"first_name":"M.R.","last_name":"Gunner","full_name":"Gunner, M.R."},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"full_name":"Singharoy, Abhishek","first_name":"Abhishek","last_name":"Singharoy"}],"related_material":{"record":[{"id":"8040","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-11T09:18:54Z","date_updated":"2023-08-22T07:49:38Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9878","year":"2020","title":"Movies","status":"public","publisher":"American Chemical Society","department":[{"_id":"LeSa"}],"month":"05","day":"20","article_processing_charge":"No","doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","mla":"Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002.","ieee":"C. Gupta et al., “Movies.” American Chemical Society, 2020.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ama":"Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002"}},{"acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Springer Nature","author":[{"full_name":"Hippe, Andreas","last_name":"Hippe","first_name":"Andreas"},{"first_name":"Stephan Alexander","last_name":"Braun","full_name":"Braun, Stephan Alexander"},{"full_name":"Oláh, Péter","last_name":"Oláh","first_name":"Péter"},{"first_name":"Peter Arne","last_name":"Gerber","full_name":"Gerber, Peter Arne"},{"full_name":"Schorr, Anne","last_name":"Schorr","first_name":"Anne"},{"full_name":"Seeliger, Stephan","last_name":"Seeliger","first_name":"Stephan"},{"full_name":"Holtz, Stephanie","first_name":"Stephanie","last_name":"Holtz"},{"full_name":"Jannasch, Katharina","last_name":"Jannasch","first_name":"Katharina"},{"full_name":"Pivarcsi, Andor","first_name":"Andor","last_name":"Pivarcsi"},{"first_name":"Bettina","last_name":"Buhren","full_name":"Buhren, Bettina"},{"first_name":"Holger","last_name":"Schrumpf","full_name":"Schrumpf, Holger"},{"full_name":"Kislat, Andreas","last_name":"Kislat","first_name":"Andreas"},{"full_name":"Bünemann, Erich","first_name":"Erich","last_name":"Bünemann"},{"full_name":"Steinhoff, Martin","last_name":"Steinhoff","first_name":"Martin"},{"full_name":"Fischer, Jens","last_name":"Fischer","first_name":"Jens"},{"last_name":"Lira","first_name":"Sérgio A.","full_name":"Lira, Sérgio A."},{"full_name":"Boukamp, Petra","last_name":"Boukamp","first_name":"Petra"},{"full_name":"Hevezi, Peter","last_name":"Hevezi","first_name":"Peter"},{"full_name":"Stoecklein, Nikolas Hendrik","first_name":"Nikolas Hendrik","last_name":"Stoecklein"},{"full_name":"Hoffmann, Thomas","last_name":"Hoffmann","first_name":"Thomas"},{"full_name":"Alves, Frauke","first_name":"Frauke","last_name":"Alves"},{"full_name":"Sleeman, Jonathan","first_name":"Jonathan","last_name":"Sleeman"},{"full_name":"Bauer, Thomas","first_name":"Thomas","last_name":"Bauer"},{"full_name":"Klufa, Jörg","last_name":"Klufa","first_name":"Jörg"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sibilia","first_name":"Maria","full_name":"Sibilia, Maria"},{"last_name":"Zlotnik","first_name":"Albert","full_name":"Zlotnik, Albert"},{"full_name":"Müller-Homey, Anja","first_name":"Anja","last_name":"Müller-Homey"},{"last_name":"Homey","first_name":"Bernhard","full_name":"Homey, Bernhard"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}],"record":[{"relation":"later_version","status":"deleted","id":"10170"}]},"date_updated":"2023-08-22T07:51:12Z","date_created":"2020-07-05T22:00:46Z","volume":123,"file_date_updated":"2021-12-02T12:35:12Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000544152500001"],"pmid":["32601464"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41416-020-0943-2","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["1532-1827"],"issn":["0007-0920"]},"_id":"8093","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","ddc":["610"],"status":"public","intvolume":" 123","oa_version":"Published Version","file":[{"file_name":"2020_BrJournalCancer_Hippe.pdf","access_level":"open_access","creator":"cchlebak","file_size":3620691,"content_type":"application/pdf","file_id":"10398","relation":"main_file","date_created":"2021-12-02T12:35:12Z","date_updated":"2021-12-02T12:35:12Z","success":1,"checksum":"05a8e65d49c3f5b8e37ac4afe68287e2"}],"type":"journal_article","abstract":[{"text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy.","lang":"eng"}],"publication":"British Journal of Cancer","citation":{"ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954."},"article_type":"original","page":"942-954","date_published":"2020-09-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1"},{"file_date_updated":"2020-11-25T15:05:04Z","ec_funded":1,"date_updated":"2023-08-22T07:51:47Z","date_created":"2020-07-05T22:00:46Z","volume":181,"author":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yngvason","first_name":"Jakob","full_name":"Yngvason, Jakob"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","year":"2020","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","month":"10","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10955-020-02586-0","isi":1,"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000543030000002"],"arxiv":["2001.07144"]},"abstract":[{"text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_JourStatPhysics_Seiringer.pdf","creator":"dernst","content_type":"application/pdf","file_size":404778,"file_id":"8812","relation":"main_file","success":1,"checksum":"5cbeef52caf18d0d952f17fed7b5545a","date_created":"2020-11-25T15:05:04Z","date_updated":"2020-11-25T15:05:04Z"}],"oa_version":"Published Version","ddc":["530"],"title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions","status":"public","intvolume":" 181","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8091","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","article_type":"original","page":"448-464","publication":"Journal of Statistical Physics","citation":{"short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464."}},{"status":"public","title":"Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence","ddc":["510"],"intvolume":" 157","_id":"8077","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":2874203,"creator":"dernst","access_level":"open_access","file_name":"2020_AppliedNumericalMath_Shehu.pdf","checksum":"87d81324a62c82baa925c009dfcb0200","date_created":"2020-07-02T09:08:59Z","date_updated":"2020-07-14T12:48:09Z","relation":"main_file","file_id":"8078"}],"type":"journal_article","abstract":[{"text":"The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.","lang":"eng"}],"article_type":"original","page":"315-337","publication":"Applied Numerical Mathematics","citation":{"ama":"Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 2020;157:315-337. doi:10.1016/j.apnum.2020.06.009","ista":"Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 157, 315–337.","ieee":"Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence,” Applied Numerical Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.","apa":"Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009.","short":"Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009."},"date_published":"2020-11-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Elsevier","acknowledgement":"The authors are grateful to the two anonymous referees for their insightful comments and suggestions which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013) (Grant agreement No. 616160).","year":"2020","date_updated":"2023-08-22T07:50:43Z","date_created":"2020-07-02T09:02:33Z","volume":157,"author":[{"full_name":"Shehu, Yekini","first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"},{"last_name":"Iyiola","first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S."}],"file_date_updated":"2020-07-14T12:48:09Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"external_id":{"isi":["000564648400018"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.apnum.2020.06.009","month":"11","publication_identifier":{"issn":["0168-9274"]}},{"date_published":"2020-06-17T00:00:00Z","publication":"ACS Applied Materials and Interfaces","citation":{"mla":"Zhang, Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces, vol. 12, no. 24, American Chemical Society, 2020, pp. 27104–11, doi:10.1021/acsami.0c04331.","short":"Y. Zhang, Y. Liu, C. Xing, T. Zhang, M. Li, M. Pacios, X. Yu, J. Arbiol, J. Llorca, D. Cadavid, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 12 (2020) 27104–27111.","chicago":"Zhang, Yu, Yu Liu, Congcong Xing, Ting Zhang, Mengyao Li, Mercè Pacios, Xiaoting Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces. American Chemical Society, 2020. https://doi.org/10.1021/acsami.0c04331.","ama":"Zhang Y, Liu Y, Xing C, et al. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 2020;12(24):27104-27111. doi:10.1021/acsami.0c04331","ista":"Zhang Y, Liu Y, Xing C, Zhang T, Li M, Pacios M, Yu X, Arbiol J, Llorca J, Cadavid D, Ibáñez M, Cabot A. 2020. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 12(24), 27104–27111.","apa":"Zhang, Y., Liu, Y., Xing, C., Zhang, T., Li, M., Pacios, M., … Cabot, A. (2020). Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.0c04331","ieee":"Y. Zhang et al., “Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices,” ACS Applied Materials and Interfaces, vol. 12, no. 24. American Chemical Society, pp. 27104–27111, 2020."},"article_type":"original","page":"27104-27111","day":"17","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"8039","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices","status":"public","intvolume":" 12","abstract":[{"text":"In the present work, we report a solution-based strategy to produce crystallographically textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric performance in the direction normal to the substrate. Our strategy is based on the formulation of a molecular precursor that can be continuously decomposed to produce a SnSe powder or printed into predefined patterns. The precursor formulation and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates. The printed layer and the bulk material obtained after hot press displays a clear preferential orientation of the crystallographic domains, resulting in an ultralow thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate. Such textured nanomaterials present highly anisotropic properties with the best thermoelectric performance in plane, i.e., in the directions parallel to the substrate, which coincide with the crystallographic bc plane of SnSe. This is an unfortunate characteristic because thermoelectric devices are designed to create/harvest temperature gradients in the direction normal to the substrate. We further demonstrate that this limitation can be overcome with the introduction of small amounts of tellurium in the precursor. The presence of tellurium allows one to reduce the band gap and increase both the charge carrier concentration and the mobility, especially the cross plane, with a minimal decrease of the Seebeck coefficient. These effects translate into record out of plane ZT values at 800 K.","lang":"eng"}],"issue":"24","type":"journal_article","doi":"10.1021/acsami.0c04331","language":[{"iso":"eng"}],"external_id":{"pmid":["32437128"],"isi":["000542925300032"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"06","publication_identifier":{"eissn":["19448252"]},"author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"Pacios, Mercè","first_name":"Mercè","last_name":"Pacios"},{"first_name":"Xiaoting","last_name":"Yu","full_name":"Yu, Xiaoting"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"date_updated":"2023-08-22T07:50:08Z","date_created":"2020-06-29T07:59:35Z","volume":12,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","ec_funded":1},{"publisher":"Springer Nature","department":[{"_id":"MaRo"}],"publication_status":"published","pmid":1,"year":"2020","volume":12,"date_updated":"2023-08-22T07:55:37Z","date_created":"2020-07-19T22:00:58Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9706"}]},"author":[{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"last_name":"Trejo-Banos","first_name":"Daniel","full_name":"Trejo-Banos, Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"first_name":"Anna J.","last_name":"Stevenson","full_name":"Stevenson, Anna J."},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"full_name":"Zhang, Qian","first_name":"Qian","last_name":"Zhang"},{"full_name":"Liewald, David C.","first_name":"David C.","last_name":"Liewald"},{"last_name":"Ritchie","first_name":"Craig W.","full_name":"Ritchie, Craig W."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"last_name":"Mcrae","first_name":"Allan F.","full_name":"Mcrae, Allan F."},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."}],"article_number":"60","file_date_updated":"2020-07-22T06:27:38Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000551778400001"],"pmid":["32641083"]},"language":[{"iso":"eng"}],"doi":"10.1186/s13073-020-00754-1","publication_identifier":{"eissn":["1756994X"]},"month":"07","intvolume":" 12","ddc":["570"],"status":"public","title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","_id":"8133","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":1136983,"content_type":"application/pdf","file_name":"2020_GenomeMedicine_Hillary.pdf","access_level":"open_access","date_created":"2020-07-22T06:27:38Z","date_updated":"2020-07-22T06:27:38Z","success":1,"file_id":"8145","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.","lang":"eng"}],"article_type":"original","citation":{"ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1","ieee":"R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020.","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).","mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1."},"publication":"Genome Medicine","date_published":"2020-07-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08"},{"abstract":[{"text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"8709","relation":"main_file","success":1,"checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","date_created":"2020-10-27T11:37:32Z","date_updated":"2020-10-27T11:37:32Z","access_level":"open_access","file_name":"2020_eLife_Gonçalves.pdf","creator":"cziletti","content_type":"application/pdf","file_size":17355867}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8127","ddc":["570"],"status":"public","title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","intvolume":" 9","day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-09-17T00:00:00Z","publication":"eLife","citation":{"short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261."},"article_type":"original","file_date_updated":"2020-10-27T11:37:32Z","ec_funded":1,"article_number":"e56261","author":[{"orcid":"0000-0002-6987-4836","last_name":"Gonçalves","first_name":"Pedro J.","full_name":"Gonçalves, Pedro J."},{"last_name":"Lueckmann","first_name":"Jan-Matthis","orcid":"0000-0003-4320-4663","full_name":"Lueckmann, Jan-Matthis"},{"full_name":"Deistler, Michael","last_name":"Deistler","first_name":"Michael","orcid":"0000-0002-3573-0404"},{"orcid":"0000-0001-6044-6627","last_name":"Nonnenmacher","first_name":"Marcel","full_name":"Nonnenmacher, Marcel"},{"full_name":"Öcal, Kaan","orcid":"0000-0002-8528-6858","last_name":"Öcal","first_name":"Kaan"},{"full_name":"Bassetto, Giacomo","first_name":"Giacomo","last_name":"Bassetto"},{"orcid":"0000-0003-4252-1608","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","last_name":"Chintaluri","first_name":"Chaitanya","full_name":"Chintaluri, Chaitanya"},{"last_name":"Podlaski","first_name":"William F.","orcid":"0000-0001-6619-7502","full_name":"Podlaski, William F."},{"full_name":"Haddad, Sara A.","first_name":"Sara A.","last_name":"Haddad","orcid":"0000-0003-0807-0823"},{"full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"},{"full_name":"Greenberg, David S.","first_name":"David S.","last_name":"Greenberg"},{"last_name":"Macke","first_name":"Jakob H.","orcid":"0000-0001-5154-8912","full_name":"Macke, Jakob H."}],"date_created":"2020-07-16T12:26:04Z","date_updated":"2023-08-22T07:54:52Z","volume":9,"year":"2020","acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"TiVo"}],"month":"09","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/eLife.56261","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000584989400001"],"pmid":["32940606"]},"quality_controlled":"1","isi":1,"project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}]},{"month":"12","publication_identifier":{"eissn":["1529-2401"]},"doi":"10.1523/JNEUROSCI.0276-20.2020","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000606706400009"],"pmid":["33168622"]},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2020-12-28T08:31:47Z","author":[{"orcid":"0000-0001-7184-7311","last_name":"Agnes","first_name":"Everton J.","full_name":"Agnes, Everton J."},{"full_name":"Luppi, Andrea I.","first_name":"Andrea I.","last_name":"Luppi"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P"}],"date_created":"2020-07-16T12:25:04Z","date_updated":"2023-08-22T07:54:26Z","volume":40,"year":"2020","pmid":1,"publication_status":"published","publisher":"Society for Neuroscience","department":[{"_id":"TiVo"}],"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-12-09T00:00:00Z","publication":"The Journal of Neuroscience","citation":{"ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649.","short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020."},"article_type":"original","page":"9634-9649","abstract":[{"text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.","lang":"eng"}],"issue":"50","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"8977","relation":"main_file","date_updated":"2020-12-28T08:31:47Z","date_created":"2020-12-28T08:31:47Z","success":1,"checksum":"7977e4dd6b89357d1a5cc88babac56da","file_name":"2020_JourNeuroscience_Agnes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2750920}],"_id":"8126","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","status":"public","ddc":["570"],"intvolume":" 40"},{"oa_version":"None","intvolume":" 5","status":"public","title":"The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8132","issue":"49","abstract":[{"text":"The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.","lang":"eng"}],"type":"journal_article","date_published":"2020-07-10T00:00:00Z","article_type":"original","citation":{"mla":"Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979, AAAS, 2020, doi:10.1126/sciimmunol.abc3979.","short":"E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel, R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S. Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B. Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei, K. Boztug, Science Immunology 5 (2020).","chicago":"Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology. AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.","ama":"Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 2020;5(49). doi:10.1126/sciimmunol.abc3979","ista":"Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 5(49), eabc3979.","ieee":"E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.","apa":"Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., … Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979"},"publication":"Science Immunology","article_processing_charge":"No","day":"10","scopus_import":"1","volume":5,"date_created":"2020-07-19T22:00:58Z","date_updated":"2023-08-22T07:56:04Z","author":[{"first_name":"Elisabeth","last_name":"Salzer","full_name":"Salzer, Elisabeth"},{"full_name":"Zoghi, Samaneh","first_name":"Samaneh","last_name":"Zoghi"},{"last_name":"Kiss","first_name":"Máté G.","full_name":"Kiss, Máté G."},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"first_name":"Christina","last_name":"Rashkova","full_name":"Rashkova, Christina"},{"last_name":"Stahnke","first_name":"Stephanie","full_name":"Stahnke, Stephanie"},{"first_name":"Matthias","last_name":"Haimel","full_name":"Haimel, Matthias"},{"full_name":"Platzer, René","first_name":"René","last_name":"Platzer"},{"last_name":"Caldera","first_name":"Michael","full_name":"Caldera, Michael"},{"full_name":"Ardy, Rico Chandra","last_name":"Ardy","first_name":"Rico Chandra"},{"full_name":"Hoeger, Birgit","last_name":"Hoeger","first_name":"Birgit"},{"full_name":"Block, Jana","last_name":"Block","first_name":"Jana"},{"full_name":"Medgyesi, David","last_name":"Medgyesi","first_name":"David"},{"full_name":"Sin, Celine","last_name":"Sin","first_name":"Celine"},{"full_name":"Shahkarami, Sepideh","last_name":"Shahkarami","first_name":"Sepideh"},{"first_name":"Renate","last_name":"Kain","full_name":"Kain, Renate"},{"first_name":"Vahid","last_name":"Ziaee","full_name":"Ziaee, Vahid"},{"first_name":"Peter","last_name":"Hammerl","full_name":"Hammerl, Peter"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"full_name":"Dupré, Loïc","last_name":"Dupré","first_name":"Loïc"},{"last_name":"Huppa","first_name":"Johannes B.","full_name":"Huppa, Johannes B."},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lomakin","first_name":"Alexis","full_name":"Lomakin, Alexis"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Binder","first_name":"Christoph J.","full_name":"Binder, Christoph J."},{"full_name":"Stradal, Theresia E.B.","last_name":"Stradal","first_name":"Theresia E.B."},{"full_name":"Rezaei, Nima","last_name":"Rezaei","first_name":"Nima"},{"first_name":"Kaan","last_name":"Boztug","full_name":"Boztug, Kaan"}],"department":[{"_id":"MiSi"}],"publisher":"AAAS","publication_status":"published","pmid":1,"year":"2020","article_number":"eabc3979","language":[{"iso":"eng"}],"doi":"10.1126/sciimmunol.abc3979","isi":1,"quality_controlled":"1","external_id":{"isi":["000546994600004"],"pmid":["32646852"]},"publication_identifier":{"eissn":["24709468"]},"month":"07"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.12629697.v1","date_published":"2020-07-09T00:00:00Z","other_data_license":"CC0 + CC BY (4.0)","day":"09","month":"07","article_processing_charge":"No","has_accepted_license":"1","year":"2020","_id":"9706","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","status":"public","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","author":[{"full_name":"Hillary, Robert F.","first_name":"Robert F.","last_name":"Hillary"},{"full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos","first_name":"Daniel"},{"last_name":"Kousathanas","first_name":"Athanasios","full_name":"Kousathanas, Athanasios"},{"last_name":"McCartney","first_name":"Daniel L.","full_name":"McCartney, Daniel L."},{"first_name":"Sarah E.","last_name":"Harris","full_name":"Harris, Sarah E."},{"last_name":"Stevenson","first_name":"Anna J.","full_name":"Stevenson, Anna J."},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"last_name":"Ojavee","first_name":"Sven Erik","full_name":"Ojavee, Sven Erik"},{"last_name":"Zhang","first_name":"Qian","full_name":"Zhang, Qian"},{"first_name":"David C.","last_name":"Liewald","full_name":"Liewald, David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","first_name":"Elliot M.","last_name":"Tucker-Drob"},{"full_name":"Wray, Naomi R.","first_name":"Naomi R.","last_name":"Wray"},{"full_name":"McRae, Allan F. ","first_name":"Allan F. ","last_name":"McRae"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"first_name":"Riccardo E. ","last_name":"Marioni","full_name":"Marioni, Riccardo E. "}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8133"}]},"date_created":"2021-07-23T08:59:15Z","date_updated":"2023-08-22T07:55:36Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).","lang":"eng"}]},{"citation":{"chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950.","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950"},"publication":"Journal of Mathematical Physics","article_type":"original","date_published":"2020-06-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8134","intvolume":" 61","title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","status":"public","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.","lang":"eng"}],"external_id":{"arxiv":["2002.08281"],"isi":["000544595100001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"oa":1,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1063/5.0005950","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00222488"]},"month":"06","year":"2020","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"last_name":"Mayer","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"volume":61,"date_created":"2020-07-19T22:00:59Z","date_updated":"2023-08-22T08:12:40Z","article_number":"061901","ec_funded":1},{"month":"07","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000552662100002"],"pmid":["32654647"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0530","article_number":"20190530","publication_status":"published","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"year":"2020","pmid":1,"date_created":"2020-07-13T03:41:39Z","date_updated":"2023-08-22T07:53:52Z","volume":375,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"scopus_import":"1","day":"12","article_processing_charge":"No","article_type":"letter_note","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.","chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.","ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530","apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530."},"date_published":"2020-07-12T00:00:00Z","type":"journal_article","issue":"1806","status":"public","title":"On the completion of speciation","intvolume":" 375","_id":"8112","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None"},{"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-09-23T00:00:00Z","publication":"Neuron","citation":{"apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031","ieee":"S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031."},"article_type":"original","page":"1160-1179.e9","abstract":[{"text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_Neuron_Laukoter.pdf","access_level":"open_access","creator":"dernst","file_size":8911830,"content_type":"application/pdf","file_id":"8828","relation":"main_file","date_updated":"2020-12-02T09:26:46Z","date_created":"2020-12-02T09:26:46Z","success":1,"checksum":"7becdc16a6317304304631087ae7dd7f"}],"_id":"8162","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Cell-type specificity of genomic imprinting in cerebral cortex","ddc":["570"],"intvolume":" 107","month":"09","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2020.06.031","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000579698700006"]},"quality_controlled":"1","isi":1,"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"file_date_updated":"2020-12-02T09:26:46Z","ec_funded":1,"author":[{"full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Beattie, Robert J","last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Penz","first_name":"Thomas","full_name":"Penz, Thomas"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock","orcid":"0000-0001-6091-3088"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/"}]},"date_created":"2020-07-23T16:03:12Z","date_updated":"2023-08-22T08:20:11Z","volume":107,"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","year":"2020","publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}]},{"ec_funded":1,"file_date_updated":"2020-07-22T08:32:55Z","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","year":"2020","volume":11,"date_created":"2020-07-21T08:58:07Z","date_updated":"2023-08-22T08:13:44Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"author":[{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"full_name":"Mazur, E","first_name":"E","last_name":"Mazur"},{"first_name":"J","last_name":"Balla","full_name":"Balla, J"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"},{"full_name":"Kalousek, P","first_name":"P","last_name":"Kalousek"},{"full_name":"Medveďová, Z","last_name":"Medveďová","first_name":"Z"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"first_name":"Y","last_name":"Wang","full_name":"Wang, Y"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","first_name":"Tomas","full_name":"Prat, Tomas"},{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K"},{"full_name":"Reinöhl, V","first_name":"V","last_name":"Reinöhl"},{"first_name":"S","last_name":"Procházka","full_name":"Procházka, S"},{"full_name":"Halouzka, R","first_name":"R","last_name":"Halouzka"},{"last_name":"Tarkowski","first_name":"P","full_name":"Tarkowski, P"},{"last_name":"Luschnig","first_name":"C","full_name":"Luschnig, C"},{"full_name":"Brewer, PB","first_name":"PB","last_name":"Brewer"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"publication_identifier":{"issn":["2041-1723"]},"month":"07","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000550062200004"],"pmid":["32665554"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17252-y","type":"journal_article","issue":"1","abstract":[{"text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.","lang":"eng"}],"intvolume":" 11","status":"public","ddc":["580"],"title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","_id":"8138","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"success":1,"date_updated":"2020-07-22T08:32:55Z","date_created":"2020-07-22T08:32:55Z","file_id":"8148","relation":"main_file","creator":"dernst","file_size":1759490,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Zhang.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","page":"3508","article_type":"original","citation":{"ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y","ieee":"J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y."},"publication":"Nature Communications","date_published":"2020-07-14T00:00:00Z"},{"month":"07","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0528","article_number":"20190528","ec_funded":1,"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"year":"2020","pmid":1,"date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:21:31Z","volume":375,"author":[{"full_name":"Kulmuni, Jonna","last_name":"Kulmuni","first_name":"Jonna"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"full_name":"Savolainen, Vincent","first_name":"Vincent","last_name":"Savolainen"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"}],"scopus_import":"1","day":"12","article_processing_charge":"No","article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","citation":{"short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528."},"date_published":"2020-07-12T00:00:00Z","type":"journal_article","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"issue":"1806","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","status":"public","intvolume":" 375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8168","oa_version":"Published Version"},{"author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Eyres, Isobel","last_name":"Eyres","first_name":"Isobel"},{"full_name":"Broquet, Thomas","first_name":"Thomas","last_name":"Broquet"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"date_updated":"2023-08-22T08:22:13Z","date_created":"2020-07-26T22:01:01Z","volume":375,"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","article_number":"20190545","doi":"10.1098/rstb.2019.0545","language":[{"iso":"eng"}],"external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"eissn":["1471-2970"]},"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8167","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","status":"public","intvolume":" 375","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"issue":"1806","type":"journal_article","date_published":"2020-07-12T00:00:00Z","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020)."},"article_type":"original","day":"12","article_processing_charge":"No","scopus_import":"1"},{"date_published":"2020-07-03T00:00:00Z","article_type":"original","citation":{"ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","ieee":"A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001.","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020)."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"03","scopus_import":"1","oa_version":"Preprint","intvolume":" 125","status":"public","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8170","issue":"1","abstract":[{"lang":"eng","text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.125.013001","project":[{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}],"external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"month":"07","volume":125,"date_updated":"2023-08-22T08:22:43Z","date_created":"2020-07-26T22:01:02Z","author":[{"first_name":"Adam S.","last_name":"Chatterley","full_name":"Chatterley, Adam S."},{"first_name":"Lars","last_name":"Christiansen","full_name":"Christiansen, Lars"},{"last_name":"Schouder","first_name":"Constant A.","full_name":"Schouder, Constant A."},{"full_name":"Jørgensen, Anders V.","first_name":"Anders V.","last_name":"Jørgensen"},{"full_name":"Shepperson, Benjamin","first_name":"Benjamin","last_name":"Shepperson"},{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","first_name":"Igor","full_name":"Cherepanov, Igor"},{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo"},{"last_name":"Zillich","first_name":"Robert E.","full_name":"Zillich, Robert E."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","year":"2020","ec_funded":1,"article_number":"013001"},{"oa_version":"Published Version","intvolume":" 12166","status":"public","title":"An SMT theory of fixed-point arithmetic","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8194","abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2020-06-24T00:00:00Z","page":"13-31","citation":{"ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2."},"publication":"Automated Reasoning","article_processing_charge":"No","day":"24","scopus_import":"1","volume":12166,"date_created":"2020-08-02T22:00:59Z","date_updated":"2023-08-22T08:27:25Z","author":[{"full_name":"Baranowski, Marek","last_name":"Baranowski","first_name":"Marek"},{"first_name":"Shaobo","last_name":"He","full_name":"He, Shaobo"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nguyen","first_name":"Thanh Son","full_name":"Nguyen, Thanh Son"},{"full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić","first_name":"Zvonimir"}],"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2020","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-51074-9_2","conference":{"name":"IJCAR: International Joint Conference on Automated Reasoning","end_date":"2020-07-04","start_date":"2020-07-01","location":"Paris, France"},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"external_id":{"isi":["000884318000002"]},"publication_identifier":{"issn":["03029743"],"isbn":["9783030510732"],"eissn":["16113349"]},"month":"06"},{"article_number":"20190544","date_updated":"2023-08-22T08:23:24Z","date_created":"2020-07-26T22:01:02Z","volume":375,"author":[{"last_name":"Shang","first_name":"Huiying","full_name":"Shang, Huiying"},{"full_name":"Hess, Jaqueline","last_name":"Hess","first_name":"Jaqueline"},{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Ingvarsson","first_name":"Pär K.","full_name":"Ingvarsson, Pär K."},{"full_name":"Liu, Jianquan","last_name":"Liu","first_name":"Jianquan"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","year":"2020","pmid":1,"month":"07","publication_identifier":{"eissn":["14712970"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0544","isi":1,"quality_controlled":"1","external_id":{"isi":["000552662100013"],"pmid":["32654641"]},"abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"issue":"1806","type":"journal_article","oa_version":"Published Version","status":"public","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","intvolume":" 375","_id":"8169","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"12","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-12T00:00:00Z","article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544","ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","ieee":"H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544."}},{"publication_identifier":{"issn":["2211-2855"]},"month":"11","external_id":{"isi":["000581738300030"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.nanoen.2020.105116","language":[{"iso":"eng"}],"article_number":"105116","year":"2020","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","department":[{"_id":"MaIb"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Yu, Xiaoting","last_name":"Yu","first_name":"Xiaoting"},{"full_name":"Liu, Junfeng","last_name":"Liu","first_name":"Junfeng"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Luo, Zhishan","last_name":"Luo","first_name":"Zhishan"},{"full_name":"Zuo, Yong","first_name":"Yong","last_name":"Zuo"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Nasiou, Déspina","last_name":"Nasiou","first_name":"Déspina"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"full_name":"Pan, Kai","last_name":"Pan","first_name":"Kai"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"full_name":"Xie, Ying","last_name":"Xie","first_name":"Ying"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"volume":77,"date_updated":"2023-08-22T08:24:05Z","date_created":"2020-08-02T22:00:57Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020, doi:10.1016/j.nanoen.2020.105116.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116.","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116","ieee":"X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020."},"publication":"Nano Energy","article_type":"original","date_published":"2020-11-01T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8189","intvolume":" 77","status":"public","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","oa_version":"None"},{"external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.1921205117","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10916490"]},"month":"07","pmid":1,"year":"2020","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","department":[{"_id":"EdHa"}],"publisher":"National Academy of Sciences","publication_status":"published","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"author":[{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","first_name":"Kasumi","full_name":"Kishi, Kasumi"},{"first_name":"Saskia I.J.","last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J."},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"volume":117,"date_updated":"2023-08-22T08:29:30Z","date_created":"2020-08-09T22:00:52Z","ec_funded":1,"file_date_updated":"2020-08-10T06:50:28Z","citation":{"mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"16969-16975","article_type":"original","date_published":"2020-07-21T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8220","intvolume":" 117","ddc":["570"],"status":"public","title":"Stem cell lineage survival as a noisy competition for niche access","file":[{"content_type":"application/pdf","file_size":1111604,"creator":"dernst","file_name":"2020_PNAS_Corominas.pdf","access_level":"open_access","date_created":"2020-08-10T06:50:28Z","date_updated":"2020-08-10T06:50:28Z","success":1,"relation":"main_file","file_id":"8223"}],"oa_version":"Published Version","type":"journal_article","issue":"29","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2020-07-29T00:00:00Z","article_type":"original","citation":{"ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020.","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015."},"publication":"SciPost Physics","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_SciPostPhys_Gulden.pdf","access_level":"open_access","content_type":"application/pdf","file_size":531137,"creator":"dernst","relation":"main_file","file_id":"8202","date_created":"2020-08-06T08:56:06Z","date_updated":"2020-08-06T08:56:06Z","success":1}],"intvolume":" 9","status":"public","title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8199","publication_identifier":{"issn":["2542-4653"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.9.1.015","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000557362300008"]},"ec_funded":1,"file_date_updated":"2020-08-06T08:56:06Z","article_number":"015","volume":9,"date_created":"2020-08-04T13:04:15Z","date_updated":"2023-08-22T08:28:24Z","author":[{"full_name":"Gulden, Tobias","orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","first_name":"Tobias"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"first_name":"Mark Spencer","last_name":"Rudner","full_name":"Rudner, Mark Spencer"},{"full_name":"Lindner, Netanel","first_name":"Netanel","last_name":"Lindner"}],"publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2020","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft"},{"publication_identifier":{"issn":["0896-6273"]},"month":"09","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2020.07.006","ec_funded":1,"file_date_updated":"2020-12-04T09:29:21Z","publisher":"Elsevier","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","volume":107,"date_updated":"2023-08-22T08:30:55Z","date_created":"2020-08-14T09:36:05Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/"}]},"author":[{"first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","article_processing_charge":"No","day":"23","page":"1212-1225","article_type":"original","citation":{"ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006."},"publication":"Neuron","date_published":"2020-09-23T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion."}],"intvolume":" 107","ddc":["570"],"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8261","file":[{"file_name":"2020_Neuron_Zhang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3011120,"file_id":"8920","relation":"main_file","date_updated":"2020-12-04T09:29:21Z","date_created":"2020-12-04T09:29:21Z","success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc"}],"oa_version":"Published Version"},{"publisher":"IEEE","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2020","acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","volume":68,"date_created":"2020-08-16T22:00:56Z","date_updated":"2023-08-22T08:40:08Z","author":[{"first_name":"Nezihe Merve","last_name":"Gurel","full_name":"Gurel, Nezihe Merve"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"full_name":"Smith, Tyler","last_name":"Smith","first_name":"Tyler"},{"last_name":"Lemmin","first_name":"Thomas","full_name":"Lemmin, Thomas"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puschel, Markus","last_name":"Puschel","first_name":"Markus"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"}],"publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]},"month":"07","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.04907"}],"external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"language":[{"iso":"eng"}],"doi":"10.1109/TSP.2020.3010355","type":"journal_article","abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"intvolume":" 68","status":"public","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8268","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"20","page":"4268-4282","article_type":"original","citation":{"chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355","ieee":"N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355"},"publication":"IEEE Transactions on Signal Processing","date_published":"2020-07-20T00:00:00Z"},{"scopus_import":"1","day":"07","article_processing_charge":"No","publication":"Molecular Plant","citation":{"mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006","ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","apa":"He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020."},"article_type":"original","page":"1238-1240","date_published":"2020-09-07T00:00:00Z","type":"journal_article","issue":"9","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8271","title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","status":"public","intvolume":" 13","oa_version":"None","month":"09","publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"external_id":{"pmid":["32688032"],"isi":["000566895400007"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.molp.2020.07.006","language":[{"iso":"eng"}],"acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier","author":[{"last_name":"He","first_name":"Peng","full_name":"He, Peng"},{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"full_name":"Xiao, Guanghui","first_name":"Guanghui","last_name":"Xiao"}],"date_created":"2020-08-16T22:00:57Z","date_updated":"2023-08-22T08:40:35Z","volume":13},{"article_type":"original","citation":{"chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602"},"publication":"Physical Review Materials","date_published":"2020-08-17T00:00:00Z","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"17","intvolume":" 4","status":"public","title":"Quantitatively consistent scale-spanning model for same-material tribocharging","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8101","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8277","date_created":"2020-08-17T15:54:20Z","date_updated":"2020-08-17T15:54:20Z","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","success":1,"file_name":"Grosjean2020.pdf","access_level":"open_access","file_size":853753,"content_type":"application/pdf","creator":"ggrosjea"}],"type":"journal_article","issue":"8","abstract":[{"text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2006.07120"],"isi":["000561897000001"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevMaterials.4.082602","publication_identifier":{"issn":["2475-9953"]},"month":"08","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"publication_status":"published","year":"2020","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","volume":4,"date_created":"2020-07-07T11:33:54Z","date_updated":"2023-08-22T08:41:32Z","related_material":{"record":[{"id":"12697","relation":"popular_science","status":"public"}]},"author":[{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","first_name":"Galien M","last_name":"Grosjean","full_name":"Grosjean, Galien M"},{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald","full_name":"Wald, Sebastian"},{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"article_number":"082602","ec_funded":1,"file_date_updated":"2020-08-17T15:54:20Z"},{"ec_funded":1,"acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail"}],"date_updated":"2023-08-22T09:00:03Z","date_created":"2020-08-30T22:01:13Z","volume":378,"month":"09","publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"external_id":{"isi":["000560620600001"],"arxiv":["1711.04285"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00220-020-03828-8","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. ","lang":"eng"}],"issue":"9","_id":"8325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Sandpile solitons via smoothing of superharmonic functions","intvolume":" 378","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Communications in Mathematical Physics","citation":{"mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8"},"article_type":"original","page":"1649-1675","date_published":"2020-09-01T00:00:00Z"},{"_id":"8318","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Key role of quinone in the mechanism of respiratory complex I","status":"public","ddc":["570"],"intvolume":" 11","oa_version":"Published Version","file":[{"creator":"cziletti","file_size":7527373,"content_type":"application/pdf","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","access_level":"open_access","date_created":"2020-08-31T13:40:00Z","date_updated":"2020-08-31T13:40:00Z","success":1,"checksum":"52b96f41d7d0db9728064c08da00d030","file_id":"8326","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I."}],"issue":"1","publication":"Nature Communications","citation":{"ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0."},"article_type":"original","date_published":"2020-08-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","year":"2020","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","last_name":"Gutierrez-Fernandez","full_name":"Gutierrez-Fernandez, Javier"},{"id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","last_name":"Kaszuba","first_name":"Karol","full_name":"Kaszuba, Karol"},{"full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S.","last_name":"Minhas"},{"full_name":"Baradaran, Rozbeh","first_name":"Rozbeh","last_name":"Baradaran"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita","full_name":"Tambalo, Margherita"},{"full_name":"Gallagher, David T.","first_name":"David T.","last_name":"Gallagher"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}]},"date_updated":"2023-08-22T09:03:00Z","date_created":"2020-08-30T22:01:10Z","volume":11,"article_number":"4135","file_date_updated":"2020-08-31T13:40:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-17957-0","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["20411723"]}},{"date_published":"2020-08-19T00:00:00Z","publication":"Molecular Biology","citation":{"ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111."},"article_type":"original","page":"475-484","day":"19","article_processing_charge":"No","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8320","title":"Expanding the genetic code: Unnatural base pairs in biological systems","status":"public","intvolume":" 54","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"issue":"4","type":"journal_article","doi":"10.1134/S0026893320040111","language":[{"iso":"eng"}],"external_id":{"isi":["000562110300001"]},"quality_controlled":"1","isi":1,"month":"08","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr","full_name":"Vlasov, Petr"},{"first_name":"P. M.","last_name":"Kolosov","full_name":"Kolosov, P. M."},{"full_name":"Shuvalova, E. Y.","first_name":"E. Y.","last_name":"Shuvalova"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"related_material":{"record":[{"id":"8321","status":"public","relation":"original"}]},"date_updated":"2023-08-22T09:01:03Z","date_created":"2020-08-30T22:01:11Z","volume":54,"acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","year":"2020","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature"},{"publication":"Molekuliarnaia biologiia","citation":{"short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541."},"article_type":"original","page":"531-541","date_published":"2020-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","_id":"8321","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","title":"Expanding the genetic code: Unnatural base pairs in biological systems","intvolume":" 54","oa_version":"None","type":"journal_article","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"issue":"4","external_id":{"pmid":["32799218"]},"quality_controlled":"1","doi":"10.31857/S0026898420040126","language":[{"iso":"rus"}],"month":"07","publication_identifier":{"issn":["00268984"]},"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"last_name":"Shuvalova","first_name":"E. Y.","full_name":"Shuvalova, E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"related_material":{"record":[{"relation":"translation","status":"public","id":"8320"}]},"date_updated":"2023-08-22T09:01:02Z","date_created":"2020-08-30T22:01:11Z","volume":54},{"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"10","doi":"10.1007/s00454-020-00237-5","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00237-5"}],"external_id":{"isi":["000561483500001"]},"oa":1,"isi":1,"author":[{"full_name":"Pach, János","first_name":"János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"volume":64,"date_created":"2020-08-30T22:01:12Z","date_updated":"2023-08-22T09:05:04Z","year":"2020","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","citation":{"short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574."},"publication":"Discrete and Computational Geometry","page":"571-574","article_type":"letter_note","type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8323","intvolume":" 64","status":"public","title":"A farewell to Ricky Pollack"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","citation":{"chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0"},"publication":"Nature Communications","article_type":"original","date_published":"2020-08-27T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8336","intvolume":" 11","status":"public","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","ddc":["580"],"oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Kubiasova.pdf","access_level":"open_access","file_size":3455704,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8357","date_created":"2020-09-10T08:05:19Z","date_updated":"2020-09-10T08:05:19Z","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","success":1}],"publication_identifier":{"eissn":["20411723"]},"month":"08","external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-020-17949-0","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"4285","ec_funded":1,"file_date_updated":"2020-09-10T08:05:19Z","pmid":1,"year":"2020","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","publisher":"Springer Nature","department":[{"_id":"EvBe"}],"publication_status":"published","author":[{"full_name":"Kubiasova, Karolina","last_name":"Kubiasova","first_name":"Karolina","orcid":"0000-0001-5630-9419","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"full_name":"Šamajová, Olga","first_name":"Olga","last_name":"Šamajová"},{"full_name":"Nisler, Jaroslav","first_name":"Jaroslav","last_name":"Nisler"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Marhavý, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavý","first_name":"Peter"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"last_name":"Zalabák","first_name":"David","full_name":"Zalabák, David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"last_name":"Galuszka","first_name":"Petr","full_name":"Galuszka, Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Plíhal","first_name":"Ondřej","full_name":"Plíhal, Ondřej"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"}],"volume":11,"date_created":"2020-09-06T22:01:12Z","date_updated":"2023-08-22T09:09:06Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8337","ddc":["580"],"status":"public","title":"Cell-surface receptors enable perception of extracellular cytokinins","intvolume":" 11","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_NatureComm_Antoniadi.pdf","file_size":3526415,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8936","checksum":"5b96f39b598de7510cfefefb819b9a6d","success":1,"date_updated":"2020-12-10T12:23:56Z","date_created":"2020-12-10T12:23:56Z"}],"scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9.","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020."},"article_type":"original","date_published":"2020-08-27T00:00:00Z","article_number":"4284","file_date_updated":"2020-12-10T12:23:56Z","ec_funded":1,"year":"2020","acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"author":[{"last_name":"Antoniadi","first_name":"Ioanna","full_name":"Antoniadi, Ioanna"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Plíhal, Ondřej","first_name":"Ondřej","last_name":"Plíhal"},{"first_name":"Radim","last_name":"Simerský","full_name":"Simerský, Radim"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"first_name":"Eduardo","last_name":"Mateo-Bonmatí","full_name":"Mateo-Bonmatí, Eduardo"},{"full_name":"Karady, Michal","first_name":"Michal","last_name":"Karady"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"full_name":"Plačková, Lenka","first_name":"Lenka","last_name":"Plačková"},{"full_name":"Opassathian, Korawit","first_name":"Korawit","last_name":"Opassathian"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Karel","last_name":"Doležal","full_name":"Doležal, Karel"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"last_name":"Turnbull","first_name":"Colin","full_name":"Turnbull, Colin"}],"date_created":"2020-09-06T22:01:13Z","date_updated":"2023-08-22T09:10:32Z","volume":11,"month":"08","publication_identifier":{"eissn":["20411723"]},"external_id":{"isi":["000567931000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"doi":"10.1038/s41467-020-17700-9","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:48:08Z","year":"2020","department":[{"_id":"StFr"}],"publisher":"IST Austria","publication_status":"submitted","related_material":{"record":[{"id":"8361","status":"public","relation":"later_version"}]},"author":[{"full_name":"Varzi, Alberto","first_name":"Alberto","last_name":"Varzi"},{"full_name":"Thanner, Katharina","last_name":"Thanner","first_name":"Katharina"},{"full_name":"Scipioni, Roberto","first_name":"Roberto","last_name":"Scipioni"},{"full_name":"Di Lecce, Daniele","last_name":"Di Lecce","first_name":"Daniele"},{"first_name":"Jusef","last_name":"Hassoun","full_name":"Hassoun, Jusef"},{"last_name":"Dörfler","first_name":"Susanne","full_name":"Dörfler, Susanne"},{"first_name":"Holger","last_name":"Altheus","full_name":"Altheus, Holger"},{"full_name":"Kaskel, Stefan","first_name":"Stefan","last_name":"Kaskel"},{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"date_created":"2020-06-30T07:37:39Z","date_updated":"2023-08-22T09:20:36Z","publication_identifier":{"issn":["2664-1690"]},"month":"07","oa":1,"doi":"10.15479/AT:ISTA:8067","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"8067","status":"public","ddc":["540"],"title":"Current status and future perspectives of Lithium metal batteries","file":[{"file_size":2612498,"content_type":"application/pdf","creator":"dernst","file_name":"20200612_JPS_review_Li_metal_submitted.pdf","access_level":"open_access","date_created":"2020-07-02T07:36:04Z","date_updated":"2020-07-14T12:48:08Z","checksum":"d183ca1465a1cbb4f8db27875cd156f7","relation":"main_file","file_id":"8076"}],"oa_version":"Published Version","keyword":["Battery","Lithium metal","Lithium-sulphur","Lithium-air","All-solid-state"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067","ieee":"A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria.","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d.","mla":"Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067.","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067."},"page":"63","date_published":"2020-07-01T00:00:00Z"},{"publication_identifier":{"issn":["0378-7753"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.jpowsour.2020.228803","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jpowsour.2020.228803"}],"external_id":{"isi":["000593857300001"]},"article_number":"228803","volume":480,"date_updated":"2023-08-22T09:20:37Z","date_created":"2020-09-10T10:48:40Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8067"}]},"author":[{"full_name":"Varzi, Alberto","last_name":"Varzi","first_name":"Alberto","orcid":"0000-0001-5069-0589"},{"full_name":"Thanner, Katharina","first_name":"Katharina","last_name":"Thanner","orcid":"0000-0001-5394-2323"},{"full_name":"Scipioni, Roberto","orcid":"0000-0003-1926-421X","first_name":"Roberto","last_name":"Scipioni"},{"first_name":"Daniele","last_name":"Di Lecce","full_name":"Di Lecce, Daniele"},{"last_name":"Hassoun","first_name":"Jusef","full_name":"Hassoun, Jusef"},{"full_name":"Dörfler, Susanne","last_name":"Dörfler","first_name":"Susanne"},{"full_name":"Altheus, Holger","first_name":"Holger","last_name":"Altheus"},{"first_name":"Stefan","last_name":"Kaskel","full_name":"Kaskel, Stefan"},{"first_name":"Christian","last_name":"Prehal","orcid":"0000-0003-0654-0940","full_name":"Prehal, Christian"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"department":[{"_id":"StFr"}],"publisher":"Elsevier","publication_status":"published","year":"2020","acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","article_processing_charge":"No","day":"31","date_published":"2020-12-31T00:00:00Z","article_type":"original","citation":{"ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803.","ieee":"A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.","mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020)."},"publication":"Journal of Power Sources","issue":"12","abstract":[{"text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 480","title":"Current status and future perspectives of lithium metal batteries","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8361"},{"status":"public","publication_status":"submitted","title":"Attosecond molecular spectroscopy and dynamics","_id":"14028","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T09:17:34Z","date_created":"2023-08-10T06:47:45Z","oa_version":"Preprint","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"type":"preprint","extern":"1","abstract":[{"text":"The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization.","lang":"eng"}],"page":"2002.02111","citation":{"short":"D.R. Baykusheva, H.J. Wörner, (n.d.).","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. Attosecond Molecular Spectroscopy and Dynamics. doi:10.48550/arXiv.2002.02111.","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Spectroscopy and Dynamics,” n.d. https://doi.org/10.48550/arXiv.2002.02111.","ama":"Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. doi:10.48550/arXiv.2002.02111","apa":"Baykusheva, D. R., & Wörner, H. J. (n.d.). Attosecond molecular spectroscopy and dynamics. https://doi.org/10.48550/arXiv.2002.02111","ieee":"D. R. Baykusheva and H. J. Wörner, “Attosecond molecular spectroscopy and dynamics.” .","ista":"Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. 10.48550/arXiv.2002.02111."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2002.02111"}],"oa":1,"external_id":{"arxiv":["2002.02111"]},"language":[{"iso":"eng"}],"date_published":"2020-02-01T00:00:00Z","doi":"10.48550/arXiv.2002.02111","month":"02","day":"01","article_processing_charge":"No"},{"file_date_updated":"2020-09-18T13:02:37Z","ec_funded":1,"article_number":"4460","date_updated":"2023-08-22T09:27:12Z","date_created":"2020-09-18T10:56:20Z","volume":11,"author":[{"full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease"},{"first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"13056","relation":"research_data","status":"public"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","year":"2020","month":"09","publication_identifier":{"issn":["2041-1723"]},"acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-18269-z","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020","name":"Quantum readout techniques and technologies"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000577280200001"]},"abstract":[{"lang":"eng","text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_NatureComm_Arnold.pdf","file_size":1002818,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8530","checksum":"88f92544889eb18bb38e25629a422a86","success":1,"date_created":"2020-09-18T13:02:37Z","date_updated":"2020-09-18T13:02:37Z"}],"oa_version":"Published Version","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","ddc":["530"],"status":"public","intvolume":" 11","_id":"8529","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"08","has_accepted_license":"1","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_published":"2020-09-08T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z."}},{"article_type":"original","publication":"ACM Transactions on Graphics","citation":{"chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466"},"date_published":"2020-07-08T00:00:00Z","scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","ddc":["000"],"title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","status":"public","intvolume":" 39","_id":"8535","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8541","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","success":1,"date_updated":"2020-09-21T07:51:44Z","date_created":"2020-09-21T07:51:44Z","access_level":"open_access","file_name":"2020_ACM_Skrivan.pdf","content_type":"application/pdf","file_size":20223953,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation."}],"issue":"4","isi":1,"quality_controlled":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"external_id":{"isi":["000583700300038"]},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3386569.3392466","month":"07","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","year":"2020","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","date_created":"2020-09-20T22:01:37Z","date_updated":"2023-08-22T09:28:27Z","volume":39,"author":[{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Andreas","last_name":"Soderstrom","full_name":"Soderstrom, Andreas"},{"full_name":"Johansson, John","last_name":"Johansson","first_name":"John"},{"full_name":"Sprenger, Christoph","last_name":"Sprenger","first_name":"Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"article_number":"65","file_date_updated":"2020-09-21T07:51:44Z","ec_funded":1},{"publication":"Annales Scientifiques de l'Ecole Normale Superieure","citation":{"ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","apa":"Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431."},"article_type":"original","page":"663-671","date_published":"2020-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","_id":"8539","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"On the K-theory stable bases of the springer resolution","intvolume":" 53","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions."},{"lang":"fre","text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. "}],"issue":"3","external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.24033/asens.2431","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["0012-9593"]},"year":"2020","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Société Mathématique de France","author":[{"last_name":"Su","first_name":"C.","full_name":"Su, C."},{"full_name":"Zhao, Gufang","first_name":"Gufang","last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhong, C.","last_name":"Zhong","first_name":"C."}],"date_updated":"2023-08-22T09:27:57Z","date_created":"2020-09-20T22:01:38Z","volume":53},{"date_published":"2020-09-25T00:00:00Z","doi":"10.1016/b978-0-12-817234-6.00009-x","language":[{"iso":"eng"}],"citation":{"ama":"Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy. In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics. 1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x","ista":"Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy. In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.","apa":"Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x","ieee":"D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,” in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and M. Quack, Eds. Elsevier, 2020, pp. 113–161.","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61, doi:10.1016/b978-0-12-817234-6.00009-x.","short":"D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161.","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-817234-6.00009-x."},"publication":"Molecular Spectroscopy and Quantum Dynamics","page":"113-161","quality_controlled":"1","publication_identifier":{"eisbn":["0128172355"],"isbn":["9780128172353"]},"article_processing_charge":"No","day":"25","month":"09","scopus_import":"1","edition":"1","author":[{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"}],"oa_version":"None","date_created":"2023-08-09T13:10:23Z","date_updated":"2023-08-22T09:25:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14000","year":"2020","publisher":"Elsevier","editor":[{"full_name":"Marquardt, Roberto","last_name":"Marquardt","first_name":"Roberto"},{"last_name":"Quack","first_name":"Martin","full_name":"Quack, Martin"}],"publication_status":"published","title":"Attosecond Molecular Dynamics and Spectroscopy","status":"public","abstract":[{"lang":"eng","text":"This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented."}],"extern":"1","type":"book_chapter"},{"_id":"13056","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","department":[{"_id":"JoFi"}],"ddc":["530"],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"author":[{"full_name":"Arnold, Georg M","first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease","full_name":"Hease, William J"},{"full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"oa_version":"Published Version","date_created":"2023-05-23T13:37:41Z","date_updated":"2023-08-22T09:27:11Z","type":"research_data_reference","abstract":[{"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.","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}],"citation":{"short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561."},"oa":1,"doi":"10.5281/ZENODO.3961561","date_published":"2020-07-27T00:00:00Z","article_processing_charge":"No","month":"07","day":"27"},{"date_published":"2020-09-01T00:00:00Z","article_type":"original","citation":{"ieee":"A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242."},"publication":"Membranes","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8583","checksum":"ceb43d7554e712dea6f36f9287271737","success":1,"date_created":"2020-09-28T11:36:50Z","date_updated":"2020-09-28T11:36:50Z","access_level":"open_access","file_name":"2020_Membranes_Andrei.pdf","file_size":4612258,"content_type":"application/pdf","creator":"dernst"}],"intvolume":" 10","status":"public","ddc":["570"],"title":"Cu homeostasis in bacteria: The ins and outs","_id":"8579","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3390/membranes10090242","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000581446000001"]},"publication_identifier":{"eissn":["20770375"]},"month":"09","volume":10,"date_updated":"2023-08-22T09:34:06Z","date_created":"2020-09-28T08:59:26Z","author":[{"first_name":"Andreea","last_name":"Andrei","full_name":"Andrei, Andreea"},{"full_name":"Öztürk, Yavuz","first_name":"Yavuz","last_name":"Öztürk"},{"last_name":"Khalfaoui-Hassani","first_name":"Bahia","full_name":"Khalfaoui-Hassani, Bahia"},{"full_name":"Rauch, Juna","last_name":"Rauch","first_name":"Juna"},{"full_name":"Marckmann, Dorian","first_name":"Dorian","last_name":"Marckmann"},{"id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Petru Iulian","last_name":"Trasnea","full_name":"Trasnea, Petru Iulian"},{"last_name":"Daldal","first_name":"Fevzi","full_name":"Daldal, Fevzi"},{"full_name":"Koch, Hans-Georg","last_name":"Koch","first_name":"Hans-Georg"}],"department":[{"_id":"LeSa"}],"publisher":"MDPI","publication_status":"published","year":"2020","file_date_updated":"2020-09-28T11:36:50Z","article_number":"242"},{"quality_controlled":"1","isi":1,"external_id":{"pmid":["32929284"],"isi":["000569299400004"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41594-020-0503-8","month":"11","publication_identifier":{"eissn":["15459985"],"issn":["15459993"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"year":"2020","acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission.","pmid":1,"date_updated":"2023-08-22T09:33:09Z","date_created":"2020-09-28T08:59:27Z","volume":27,"author":[{"full_name":"Pinke, Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Pinke"},{"full_name":"Zhou, Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1864-8951","first_name":"Long","last_name":"Zhou"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"article_type":"original","page":"1077-1085","publication":"Nature Structural and Molecular Biology","citation":{"chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.","mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8.","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.","ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020.","apa":"Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-020-0503-8","ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085. doi:10.1038/s41594-020-0503-8"},"date_published":"2020-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","status":"public","intvolume":" 27","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8581","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine."}],"issue":"11"},{"conference":{"name":"ESGCO: European Study Group on Cardiovascular Oscillations","start_date":"2020-07-15","location":"Pisa, Italy","end_date":"2020-07-15"},"date_published":"2020-08-01T00:00:00Z","doi":"10.1109/ESGCO49734.2020.9158054","language":[{"iso":"eng"}],"publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","citation":{"short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.","chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054","apa":"Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054."},"external_id":{"isi":["000621172600045"]},"quality_controlled":"1","isi":1,"month":"08","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9781728157511"]},"scopus_import":"1","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"last_name":"Graff","first_name":"Beata","full_name":"Graff, Beata"},{"last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"date_created":"2020-09-28T08:59:27Z","date_updated":"2023-08-22T09:33:34Z","oa_version":"None","_id":"8580","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2020","publication_status":"published","title":"The application of persistent homology in the analysis of heart rate variability","status":"public","publisher":"IEEE","department":[{"_id":"HeEd"}],"abstract":[{"text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.","lang":"eng"}],"article_number":"9158054","type":"conference"},{"acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Tian, Anhao","first_name":"Anhao","last_name":"Tian"},{"last_name":"Kang","first_name":"Bo","full_name":"Kang, Bo"},{"first_name":"Baizhou","last_name":"Li","full_name":"Li, Baizhou"},{"full_name":"Qiu, Biying","first_name":"Biying","last_name":"Qiu"},{"last_name":"Jiang","first_name":"Wenhong","full_name":"Jiang, Wenhong"},{"last_name":"Shao","first_name":"Fangjie","full_name":"Shao, Fangjie"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"first_name":"Rui","last_name":"Liu","full_name":"Liu, Rui"},{"first_name":"Chengwei","last_name":"Cai","full_name":"Cai, Chengwei"},{"last_name":"Jing","first_name":"Rui","full_name":"Jing, Rui"},{"first_name":"Wei","last_name":"Wang","full_name":"Wang, Wei"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"first_name":"Qinghui","last_name":"Liang","full_name":"Liang, Qinghui"},{"full_name":"Bao, Lili","last_name":"Bao","first_name":"Lili"},{"last_name":"Man","first_name":"Jianghong","full_name":"Man, Jianghong"},{"full_name":"Wang, Yan","last_name":"Wang","first_name":"Yan"},{"last_name":"Shi","first_name":"Yu","full_name":"Shi, Yu"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"last_name":"Yang","first_name":"Minmin","full_name":"Yang, Minmin"},{"first_name":"Lisha","last_name":"Wang","full_name":"Wang, Lisha"},{"full_name":"Zhang, Jianmin","last_name":"Zhang","first_name":"Jianmin"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"first_name":"Ying‐Jie","last_name":"Wang","full_name":"Wang, Ying‐Jie"},{"first_name":"Chong","last_name":"Liu","full_name":"Liu, Chong"}],"volume":7,"date_created":"2020-10-01T09:44:13Z","date_updated":"2023-08-22T09:53:01Z","article_number":"2001724","ec_funded":1,"file_date_updated":"2020-12-10T14:07:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000573860700001"]},"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"quality_controlled":"1","isi":1,"doi":"10.1002/advs.202001724","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2198-3844"]},"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8592","intvolume":" 7","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","ddc":["570"],"status":"public","file":[{"date_updated":"2020-12-10T14:07:24Z","date_created":"2020-12-10T14:07:24Z","checksum":"92818c23ecc70e35acfa671f3cfb9909","success":1,"relation":"main_file","file_id":"8938","file_size":7835833,"content_type":"application/pdf","creator":"dernst","file_name":"2020_AdvScience_Tian.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"21","abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"citation":{"ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020)."},"publication":"Advanced Science","article_type":"original","date_published":"2020-11-04T00:00:00Z","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"article_processing_charge":"No","has_accepted_license":"1","day":"04"},{"external_id":{"isi":["000573756600004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-18610-6","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2041-1723"]},"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"StFr"}],"author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","first_name":"Harald","last_name":"Fitzek"},{"full_name":"Kothleitner, Gerald","first_name":"Gerald","last_name":"Kothleitner"},{"full_name":"Presser, Volker","first_name":"Volker","last_name":"Presser"},{"last_name":"Gollas","first_name":"Bernhard","full_name":"Gollas, Bernhard"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"last_name":"Abbas","first_name":"Qamar","full_name":"Abbas, Qamar"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"date_created":"2020-09-25T07:23:13Z","date_updated":"2023-08-22T09:37:24Z","volume":11,"article_number":"4838","file_date_updated":"2020-09-28T13:16:15Z","publication":"Nature Communications","citation":{"chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6"},"article_type":"original","date_published":"2020-09-24T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"day":"24","article_processing_charge":"No","has_accepted_license":"1","_id":"8568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","intvolume":" 11","file":[{"relation":"main_file","file_id":"8585","date_updated":"2020-09-28T13:16:15Z","date_created":"2020-09-28T13:16:15Z","checksum":"eada7bc8dd16a49390137cff882ef328","success":1,"file_name":"2020_NatureComm_Prehal.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1822469,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}]},{"abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_ScientificReport_Deichler.pdf","file_size":3906744,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8651","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1,"date_created":"2020-10-12T12:39:10Z","date_updated":"2020-10-12T12:39:10Z"}],"_id":"8643","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","intvolume":" 10","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","publication":"Scientific Reports","citation":{"ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0."},"article_type":"original","file_date_updated":"2020-10-12T12:39:10Z","article_number":"16220","author":[{"first_name":"Alfonso","last_name":"Deichler","full_name":"Deichler, Alfonso"},{"full_name":"Carrasco, Denisse","first_name":"Denisse","last_name":"Carrasco"},{"full_name":"Lopez-Jury, Luciana","last_name":"Lopez-Jury","first_name":"Luciana"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marquez","first_name":"Natalia","full_name":"Marquez, Natalia"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"},{"full_name":"Marin, Gonzalo","first_name":"Gonzalo","last_name":"Marin"}],"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:58:21Z","volume":10,"acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaJö"}],"month":"10","publication_identifier":{"eissn":["20452322"]},"doi":"10.1038/s41598-020-72848-0","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577142600032"]},"oa":1,"isi":1,"quality_controlled":"1"},{"day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-03-15T00:00:00Z","publication":"Bioinformatics","citation":{"ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841."},"article_type":"original","page":"1960-1962","abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"8649","date_updated":"2020-10-12T12:02:09Z","date_created":"2020-10-12T12:02:09Z","checksum":"21d6f71839deb3b83e4a356193f72767","success":1,"file_name":"2020_Bioinformatics_Esteban.pdf","access_level":"open_access","file_size":308341,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"8645","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000","570"],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","status":"public","intvolume":" 36","month":"03","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"doi":"10.1093/bioinformatics/btz841","language":[{"iso":"eng"}],"external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"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)"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-10-12T12:02:09Z","ec_funded":1,"author":[{"full_name":"Esteban, Laura A","first_name":"Laura A","last_name":"Esteban"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"full_name":"Bobrovskiy, Daniil M","last_name":"Bobrovskiy","first_name":"Daniil M"},{"full_name":"Leleytner, Gregory","first_name":"Gregory","last_name":"Leleytner"},{"first_name":"Natalya S","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N ","last_name":"Ivankov","first_name":"Dmitry N "}],"date_updated":"2023-08-22T09:57:29Z","date_created":"2020-10-11T22:01:14Z","volume":36,"acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","year":"2020","pmid":1,"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"FyKo"}]},{"date_published":"2020-09-23T00:00:00Z","article_type":"original","publication":"Physical Biology","citation":{"chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db.","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","short":"J. Merrin, Physical Biology 17 (2020).","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db","ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db"},"day":"23","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_PhysBio_Merrin.pdf","creator":"dernst","content_type":"application/pdf","file_size":1667111,"file_id":"8609","relation":"main_file","success":1,"checksum":"fec9bdd355ed349f09990faab20838a7","date_updated":"2020-10-05T13:53:59Z","date_created":"2020-10-05T13:53:59Z"}],"ddc":["510","570"],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","status":"public","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8597","abstract":[{"lang":"eng","text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy."}],"issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1088/1478-3975/abb2db","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000575539700001"]},"month":"09","publication_identifier":{"eissn":["14783975"]},"date_updated":"2023-08-22T09:53:29Z","date_created":"2020-10-04T22:01:35Z","volume":17,"author":[{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"}],"publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"IOP Publishing","year":"2020","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","file_date_updated":"2020-10-05T13:53:59Z","article_number":"065005"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2020.08.030","quality_controlled":"1","isi":1,"external_id":{"isi":["000603428000010"],"pmid":["32976770"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"12","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"date_created":"2020-10-18T22:01:38Z","date_updated":"2023-08-22T09:59:29Z","volume":108,"author":[{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"last_name":"Bard","first_name":"Lucie","full_name":"Bard, Lucie"},{"last_name":"Panatier","first_name":"Aude","full_name":"Panatier, Aude"},{"full_name":"Reynolds, James P.","first_name":"James P.","last_name":"Reynolds"},{"last_name":"Kopach","first_name":"Olga","full_name":"Kopach, Olga"},{"first_name":"Nikolay I.","last_name":"Medvedev","full_name":"Medvedev, Nikolay I."},{"full_name":"Minge, Daniel","first_name":"Daniel","last_name":"Minge"},{"last_name":"Herde","first_name":"Michel K.","full_name":"Herde, Michel K."},{"full_name":"Anders, Stefanie","last_name":"Anders","first_name":"Stefanie"},{"full_name":"Kraev, Igor","last_name":"Kraev","first_name":"Igor"},{"last_name":"Heller","first_name":"Janosch P.","full_name":"Heller, Janosch P."},{"last_name":"Rama","first_name":"Sylvain","full_name":"Rama, Sylvain"},{"full_name":"Zheng, Kaiyu","last_name":"Zheng","first_name":"Kaiyu"},{"full_name":"Jensen, Thomas P.","last_name":"Jensen","first_name":"Thomas P."},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez-Romero","first_name":"Inmaculada","full_name":"Sanchez-Romero, Inmaculada"},{"last_name":"Jackson","first_name":"Colin J.","full_name":"Jackson, Colin J."},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"first_name":"Ole Petter","last_name":"Ottersen","full_name":"Ottersen, Ole Petter"},{"last_name":"Nagelhus","first_name":"Erlend Arnulf","full_name":"Nagelhus, Erlend Arnulf"},{"full_name":"Oliet, Stephane H.R.","first_name":"Stephane H.R.","last_name":"Oliet"},{"first_name":"Michael G.","last_name":"Stewart","full_name":"Stewart, Michael G."},{"full_name":"Nägerl, U. VAlentin","first_name":"U. VAlentin","last_name":"Nägerl"},{"full_name":"Rusakov, Dmitri A. ","first_name":"Dmitri A. ","last_name":"Rusakov"}],"publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Elsevier","year":"2020","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","pmid":1,"file_date_updated":"2020-12-10T14:42:09Z","date_published":"2020-12-09T00:00:00Z","article_type":"original","page":"P919-936.E11","publication":"Neuron","citation":{"ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030","ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.","chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030."},"day":"09","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_Neuron_Henneberger.pdf","file_size":7518960,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8939","checksum":"054562bb50165ef9a1f46631c1c5e36b","success":1,"date_updated":"2020-12-10T14:42:09Z","date_created":"2020-12-10T14:42:09Z"}],"ddc":["570"],"status":"public","title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","intvolume":" 108","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8674","abstract":[{"text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.","lang":"eng"}],"issue":"5","type":"journal_article"},{"date_published":"2020-10-09T00:00:00Z","publication":"Communications Physics","citation":{"chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.","short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8"},"article_type":"original","day":"09","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8662","date_updated":"2020-10-14T15:16:28Z","date_created":"2020-10-14T15:16:28Z","checksum":"60cd35b99f0780acffc7b6060e49ec8b","success":1,"file_name":"2020_CommPhysics_Ghazaryan.pdf","access_level":"open_access","file_size":1462934,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8652","status":"public","ddc":["530"],"title":"Filtering spins by scattering from a lattice of point magnets","intvolume":" 3","abstract":[{"lang":"eng","text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules."}],"type":"journal_article","doi":"10.1038/s42005-020-00445-8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000581681000001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"month":"10","publication_identifier":{"issn":["2399-3650"]},"author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-10-13T09:48:59Z","date_updated":"2023-08-22T09:58:46Z","volume":3,"acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","year":"2020","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Springer Nature","file_date_updated":"2020-10-14T15:16:28Z","ec_funded":1,"article_number":"178"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","citation":{"chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3"},"publication":"Nature Communications","article_type":"original","date_published":"2020-10-07T00:00:00Z","type":"journal_article","abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8669","intvolume":" 11","title":"Tracing the cellular basis of islet specification in mouse pancreas","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Sznurkowska.pdf","access_level":"open_access","creator":"dernst","file_size":5540540,"content_type":"application/pdf","file_id":"8677","relation":"main_file","date_created":"2020-10-19T11:27:46Z","date_updated":"2020-10-19T11:27:46Z","success":1,"checksum":"0ecc0eab72d2d50694852579611a6624"}],"publication_identifier":{"eissn":["20411723"]},"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-020-18837-3","language":[{"iso":"eng"}],"article_number":"5037","file_date_updated":"2020-10-19T11:27:46Z","pmid":1,"year":"2020","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"first_name":"Magdalena K.","last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena K."},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Azzarelli, Roberta","last_name":"Azzarelli","first_name":"Roberta"},{"full_name":"Chatzeli, Lemonia","first_name":"Lemonia","last_name":"Chatzeli"},{"full_name":"Ikeda, Tatsuro","first_name":"Tatsuro","last_name":"Ikeda"},{"full_name":"Yoshida, Shosei","first_name":"Shosei","last_name":"Yoshida"},{"full_name":"Philpott, Anna","first_name":"Anna","last_name":"Philpott"},{"last_name":"Simons","first_name":"Benjamin D","full_name":"Simons, Benjamin D"}],"volume":11,"date_created":"2020-10-18T22:01:35Z","date_updated":"2023-08-22T10:18:17Z"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","page":"195-208","article_type":"original","citation":{"ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208.","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001."},"publication":"Developmental Cell","date_published":"2020-10-26T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions."}],"intvolume":" 55","ddc":["570"],"title":"Abscission couples cell division to embryonic stem cell fate","status":"public","_id":"8672","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_DevelopmCell_Chaigne.pdf","content_type":"application/pdf","file_size":6929686,"creator":"dernst","relation":"main_file","file_id":"9086","checksum":"88e1a031a61689165d19a19c2f16d795","success":1,"date_updated":"2021-02-04T10:20:02Z","date_created":"2021-02-04T10:20:02Z"}],"publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"month":"10","quality_controlled":"1","isi":1,"external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.09.001","file_date_updated":"2021-02-04T10:20:02Z","department":[{"_id":"EdHa"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","volume":55,"date_created":"2020-10-18T22:01:37Z","date_updated":"2023-08-22T10:16:58Z","author":[{"first_name":"Agathe","last_name":"Chaigne","full_name":"Chaigne, Agathe"},{"last_name":"Labouesse","first_name":"Céline","full_name":"Labouesse, Céline"},{"last_name":"White","first_name":"Ian J.","full_name":"White, Ian J."},{"first_name":"Meghan","last_name":"Agnew","full_name":"Agnew, Meghan"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Chalut","first_name":"Kevin J.","full_name":"Chalut, Kevin J."},{"full_name":"Paluch, Ewa K.","last_name":"Paluch","first_name":"Ewa K."}]},{"file_date_updated":"2020-10-27T12:09:57Z","license":"https://creativecommons.org/licenses/by/3.0/","year":"2020","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"IOP Publishing","author":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"first_name":"Michael","last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael"}],"date_created":"2020-10-25T23:01:16Z","date_updated":"2023-08-22T10:38:38Z","volume":33,"month":"11","publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000576492700001"],"arxiv":["1906.12245"]},"quality_controlled":"1","isi":1,"doi":"10.1088/1361-6544/ab9728","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.","lang":"eng"}],"issue":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8697","status":"public","ddc":["510"],"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","intvolume":" 33","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_Nonlinearity_Fischer.pdf","creator":"cziletti","content_type":"application/pdf","file_size":1223899,"file_id":"8710","relation":"main_file","success":1,"checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","date_updated":"2020-10-27T12:09:57Z","date_created":"2020-10-27T12:09:57Z"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Nonlinearity","citation":{"ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.","apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772."},"article_type":"original","page":"5733-5772","date_published":"2020-11-01T00:00:00Z"},{"year":"2020","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"American Association for the Advancement of Science","author":[{"full_name":"Tsai, Tony Y.-C.","first_name":"Tony Y.-C.","last_name":"Tsai"},{"last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng"},{"full_name":"Colak-Champollion, Tugba","first_name":"Tugba","last_name":"Colak-Champollion"},{"last_name":"Knaut","first_name":"Holger","full_name":"Knaut, Holger"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Megason","first_name":"Sean G.","full_name":"Megason, Sean G."}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/sticking-together/"}]},"date_updated":"2023-08-22T10:36:35Z","date_created":"2020-10-19T14:09:38Z","volume":370,"ec_funded":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/803635v1","open_access":"1"}],"oa":1,"external_id":{"isi":["000579169000053"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"doi":"10.1126/science.aba6637","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8680","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","status":"public","intvolume":" 370","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning."}],"issue":"6512","publication":"Science","citation":{"short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116."},"article_type":"original","page":"113-116","date_published":"2020-10-02T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"day":"02","article_processing_charge":"No"},{"doi":"10.1038/s41588-020-00712-y","language":[{"iso":"eng"}],"external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["10614036"],"eissn":["15461718"]},"month":"10","author":[{"first_name":"Silvia","last_name":" Galan","full_name":" Galan, Silvia"},{"last_name":"Machnik","first_name":"Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N"},{"full_name":"Kruse, Kai","first_name":"Kai","last_name":"Kruse"},{"first_name":"Noelia","last_name":"Díaz","full_name":"Díaz, Noelia"},{"full_name":"Marti-Renom, Marc A","first_name":"Marc A","last_name":"Marti-Renom"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"volume":52,"date_updated":"2023-08-22T10:37:10Z","date_created":"2020-10-25T23:01:20Z","pmid":1,"year":"2020","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","date_published":"2020-10-19T00:00:00Z","citation":{"ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y.","short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y."},"publication":"Nature Genetics","page":"1247-1255","article_type":"original","article_processing_charge":"No","day":"19","scopus_import":"1","oa_version":"None","_id":"8707","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 52","status":"public","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","abstract":[{"lang":"eng","text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data."}],"type":"journal_article"},{"date_published":"2020-10-01T00:00:00Z","citation":{"mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652.","chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3","ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020.","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3"},"publication":"Nature Machine Intelligence","page":"642-652","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8679","intvolume":" 2","title":"Neural circuit policies enabling auditable autonomy","status":"public","abstract":[{"text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s42256-020-00237-3","language":[{"iso":"eng"}],"external_id":{"isi":["000583337200011"]},"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2522-5839"]},"month":"10","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-deep-learning-models/"}]},"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"volume":2,"date_created":"2020-10-19T13:46:06Z","date_updated":"2023-08-22T10:36:06Z","year":"2020","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published"},{"doi":"10.1063/5.0022787","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06644"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00222488"]},"month":"10","author":[{"full_name":"Zhang, Haonan","last_name":"Zhang","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"volume":61,"date_created":"2020-10-18T22:01:36Z","date_updated":"2023-08-22T10:32:29Z","acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","year":"2020","department":[{"_id":"JaMa"}],"publisher":"AIP Publishing","publication_status":"published","ec_funded":1,"article_number":"102201","date_published":"2020-10-01T00:00:00Z","citation":{"ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787."},"publication":"Journal of Mathematical Physics","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"8670","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 61","status":"public","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","issue":"10","abstract":[{"text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].","lang":"eng"}],"type":"journal_article"},{"month":"10","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1912804117","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"file_date_updated":"2020-10-27T14:57:50Z","date_updated":"2023-08-22T12:11:23Z","date_created":"2020-10-25T23:01:16Z","volume":117,"author":[{"last_name":"Maoz","first_name":"Ori","full_name":"Maoz, Ori"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Esteki, Mohamad Saleh","last_name":"Esteki","first_name":"Mohamad Saleh"},{"full_name":"Kiani, Roozbeh","first_name":"Roozbeh","last_name":"Kiani"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","year":"2020","pmid":1,"day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-06T00:00:00Z","article_type":"original","page":"25066-25073","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073."},"abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"issue":"40","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8713","checksum":"c6a24fdecf3f28faf447078e7a274a88","success":1,"date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","access_level":"open_access","file_name":"2020_PNAS_Maoz.pdf","content_type":"application/pdf","file_size":1755359,"creator":"cziletti"}],"title":"Learning probabilistic neural representations with randomly connected circuits","ddc":["570"],"status":"public","intvolume":" 117","_id":"8698","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-22T10:40:15Z","date_created":"2020-10-25T23:01:19Z","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","year":"2020","file_date_updated":"2020-11-06T10:58:49Z","language":[{"iso":"eng"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2020-05-31","location":"Paris, France","end_date":"2020-08-31"},"doi":"10.1109/ICRA40945.2020.9196608","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000712319503110"]},"month":"05","publication_identifier":{"issn":["10504729"],"isbn":["9781728173955"]},"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8733","date_updated":"2020-11-06T10:58:49Z","date_created":"2020-11-06T10:58:49Z","checksum":"fccf7b986ac78046918a298cc6849a50","success":1,"file_name":"2020_ICRA_Lechner.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1070010,"creator":"dernst"}],"status":"public","title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","ddc":["000"],"_id":"8704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.","lang":"eng"}],"alternative_title":["ICRA"],"type":"conference","date_published":"2020-05-01T00:00:00Z","page":"5446-5452","publication":"Proceedings - IEEE International Conference on Robotics and Automation","citation":{"ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608","apa":"Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452.","ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"related_material":{"record":[{"id":"8701","relation":"original","status":"public"}]},"author":[{"full_name":"Sokolova, E. E.","last_name":"Sokolova","first_name":"E. E."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr","full_name":"Vlasov, Petr"},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"last_name":"Shuvalov","first_name":"A. V.","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"volume":54,"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T10:39:38Z","year":"2020","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","doi":"10.1134/S0026893320050088","language":[{"iso":"eng"}],"external_id":{"isi":["000579441200009"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"month":"09","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8700","intvolume":" 54","status":"public","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","issue":"5","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"type":"journal_article","date_published":"2020-09-01T00:00:00Z","citation":{"short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748."},"publication":"Molecular Biology","page":"739-748","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","publication_status":"published","pmid":1,"year":"2020","volume":54,"date_updated":"2023-08-22T10:39:37Z","date_created":"2020-10-25T23:01:17Z","related_material":{"record":[{"relation":"translation","status":"public","id":"8700"}]},"author":[{"last_name":"Sokolova","first_name":"E. E.","full_name":"Sokolova, E. E."},{"full_name":"Vlasov, Petr","first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"first_name":"A. V.","last_name":"Shuvalov","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"publication_identifier":{"issn":["00268984"]},"month":"09","quality_controlled":"1","external_id":{"pmid":["33009793"]},"language":[{"iso":"rus"}],"doi":"10.31857/S0026898420050080","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"intvolume":" 54","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8701","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","page":"837-848","article_type":"original","citation":{"ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080."},"publication":"Molekuliarnaia biologiia","date_published":"2020-09-01T00:00:00Z"},{"day":"12","month":"11","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-11-12T00:00:00Z","doi":"10.48550/arXiv.2011.06630","publication":"arXiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"citation":{"short":"J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.).","mla":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630.","chicago":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630.","ama":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630","apa":"Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630","ieee":"J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. .","ista":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630."},"external_id":{"arxiv":["2011.06630"]},"oa":1,"abstract":[{"text":"A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources.","lang":"eng"}],"article_number":"2011.06630","type":"preprint","date_created":"2023-08-21T10:10:41Z","date_updated":"2023-08-22T11:03:00Z","oa_version":"Preprint","author":[{"full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith","first_name":"Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith"},{"full_name":"Everson, Rosa Wallace","first_name":"Rosa Wallace","last_name":"Everson"},{"first_name":"Enrico Ramirez-Ruiz","last_name":"Enrico Ramirez-Ruiz","full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz"},{"full_name":"Mink, Selma E. de","last_name":"Mink","first_name":"Selma E. de"},{"full_name":"Son, Lieke A. C. van","last_name":"Son","first_name":"Lieke A. C. van"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter"},{"first_name":"Stefan","last_name":"Zellmann","full_name":"Zellmann, Stefan"},{"last_name":"Alejandro Vigna-Gómez","first_name":"Alejandro Vigna-Gómez","full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez"},{"first_name":"Mathieu","last_name":"Renzo","full_name":"Renzo, Mathieu"},{"first_name":"Samantha","last_name":"Wu","full_name":"Wu, Samantha"},{"last_name":"Schrøder","first_name":"Sophie L.","full_name":"Schrøder, Sophie L."},{"first_name":"Ryan J.","last_name":"Foley","full_name":"Foley, Ryan J."},{"first_name":"Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith","full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith"}],"title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","status":"public","publication_status":"submitted","year":"2020","_id":"14096","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770."},"article_type":"original","page":"24764-24770","date_published":"2020-10-06T00:00:00Z","type":"journal_article","abstract":[{"text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling.","lang":"eng"}],"issue":"40","_id":"8699","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","intvolume":" 117","file":[{"file_id":"8715","relation":"main_file","date_updated":"2020-10-28T11:53:12Z","date_created":"2020-10-28T11:53:12Z","success":1,"checksum":"1638fa36b442e2868576c6dd7d6dc505","file_name":"2020_PNAS_Paris.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":1176522}],"oa_version":"Published Version","month":"10","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2009.12262"],"isi":["000579059100029"],"pmid":["32958669"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1073/pnas.2012043117","language":[{"iso":"eng"}],"file_date_updated":"2020-10-28T11:53:12Z","ec_funded":1,"acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","year":"2020","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MiLe"}],"author":[{"full_name":"Paris, Eugenio","first_name":"Eugenio","last_name":"Paris"},{"full_name":"Tseng, Yi","last_name":"Tseng","first_name":"Yi"},{"id":"8275014E-6063-11E9-9B7F-6338E6697425","orcid":"0000-0003-0853-8182","first_name":"Ekaterina","last_name":"Paerschke","full_name":"Paerschke, Ekaterina"},{"full_name":"Zhang, Wenliang","first_name":"Wenliang","last_name":"Zhang"},{"first_name":"Mary H","last_name":"Upton","full_name":"Upton, Mary H"},{"full_name":"Efimenko, Anna","first_name":"Anna","last_name":"Efimenko"},{"first_name":"Katharina","last_name":"Rolfs","full_name":"Rolfs, Katharina"},{"full_name":"McNally, Daniel E","first_name":"Daniel E","last_name":"McNally"},{"full_name":"Maurel, Laura","first_name":"Laura","last_name":"Maurel"},{"last_name":"Naamneh","first_name":"Muntaser","full_name":"Naamneh, Muntaser"},{"full_name":"Caputo, Marco","last_name":"Caputo","first_name":"Marco"},{"last_name":"Strocov","first_name":"Vladimir N","full_name":"Strocov, Vladimir N"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"full_name":"Casa, Diego","last_name":"Casa","first_name":"Diego"},{"last_name":"Schneider","first_name":"Christof W","full_name":"Schneider, Christof W"},{"full_name":"Pomjakushina, Ekaterina","last_name":"Pomjakushina","first_name":"Ekaterina"},{"full_name":"Wohlfeld, Krzysztof","last_name":"Wohlfeld","first_name":"Krzysztof"},{"first_name":"Milan","last_name":"Radovic","full_name":"Radovic, Milan"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T12:11:52Z","volume":117},{"type":"journal_article","issue":"6516","abstract":[{"lang":"eng","text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions."}],"intvolume":" 370","ddc":["572"],"status":"public","title":"The coupling mechanism of mammalian respiratory complex I","_id":"8737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"658ba90979ca9528a2efdfac8547047a","success":1,"date_created":"2020-11-26T18:47:58Z","date_updated":"2020-11-26T18:47:58Z","relation":"main_file","file_id":"8820","content_type":"application/pdf","file_size":7618987,"creator":"lsazanov","access_level":"open_access","file_name":"Full_manuscript_with_SI_opt_red.pdf"}],"oa_version":"Submitted Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","article_type":"original","citation":{"chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209.","ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","apa":"Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209","ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209"},"publication":"Science","date_published":"2020-10-30T00:00:00Z","article_number":"eabc4209","ec_funded":1,"file_date_updated":"2020-11-26T18:47:58Z","department":[{"_id":"LeSa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","volume":370,"date_updated":"2023-08-22T12:35:38Z","date_created":"2020-11-08T23:01:23Z","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut","full_name":"Kampjut, Domen"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["10959203"]},"month":"10","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["32972993"],"isi":["000583031800004"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1126/science.abc4209"},{"day":"01","article_processing_charge":"No","date_published":"2020-02-01T00:00:00Z","publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.","short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61.","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61.","ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528"},"page":"45-61","abstract":[{"lang":"eng","text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy."}],"type":"conference","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8722","title":"Taming unbalanced training workloads in deep learning with partial collective operations","status":"public","month":"02","conference":{"location":"San Diego, CA, United States","start_date":"2020-02-22","end_date":"2020-02-26","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3332466.3374528","language":[{"iso":"eng"}],"external_id":{"isi":["000564476500004"],"arxiv":["1908.04207"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.04207"}],"quality_controlled":"1","isi":1,"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"ec_funded":1,"author":[{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"first_name":"Tal Ben-Nun","last_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun"},{"first_name":"Salvatore Di","last_name":"Girolamo","full_name":"Girolamo, Salvatore Di"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"}],"date_updated":"2023-08-22T12:13:48Z","date_created":"2020-11-05T15:25:30Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}]},{"file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","volume":11,"date_updated":"2023-08-22T12:36:07Z","date_created":"2020-11-09T07:49:36Z","author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"full_name":"Mao, Jiafei","first_name":"Jiafei","last_name":"Mao"},{"last_name":"Reitz","first_name":"Julian","full_name":"Reitz, Julian"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Jakob","last_name":"Meier-Credo","full_name":"Meier-Credo, Jakob"},{"first_name":"Krishna","last_name":"Saxena","full_name":"Saxena, Krishna"},{"first_name":"Florian","last_name":"Buhr","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","first_name":"Julian D.","last_name":"Langer"},{"full_name":"Blackledge, Martin","first_name":"Martin","last_name":"Blackledge"},{"full_name":"Frangakis, Achilleas S.","last_name":"Frangakis","first_name":"Achilleas S."},{"full_name":"Glaubitz, Clemens","last_name":"Glaubitz","first_name":"Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"department":[{"_id":"EM-Fac"}],"publisher":"Springer Nature","publication_status":"published","year":"2020","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","publication_identifier":{"issn":["2041-1723"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19372-x","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000592028600001"]},"abstract":[{"lang":"eng","text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding."}],"type":"journal_article","file":[{"creator":"dernst","file_size":1670898,"content_type":"application/pdf","file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","date_created":"2020-11-09T07:56:24Z","date_updated":"2020-11-09T07:56:24Z","success":1,"checksum":"b2688f0347e69e6629bba582077278c5","file_id":"8745","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 11","ddc":["570"],"status":"public","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8744","has_accepted_license":"1","article_processing_charge":"No","day":"04","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","date_published":"2020-11-04T00:00:00Z","article_type":"original","citation":{"short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x.","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569."},"publication":"Nature Communications"},{"oa_version":"None","title":"Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks","status":"public","intvolume":" 8","_id":"8747","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3.","lang":"eng"}],"issue":"40","type":"journal_article","date_published":"2020-10-28T00:00:00Z","article_type":"original","page":"14092-14099","publication":"Journal of Materials Chemistry C","citation":{"chicago":"Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol, Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B.","mla":"Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B.","short":"Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid, M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099.","ista":"Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M, Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099.","apa":"Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot, A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/D0TC02182B","ieee":"Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” Journal of Materials Chemistry C, vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020.","ama":"Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 2020;8(40):14092-14099. doi:10.1039/D0TC02182B"},"day":"28","article_processing_charge":"No","scopus_import":"1","date_created":"2020-11-09T08:37:51Z","date_updated":"2023-08-22T12:41:05Z","volume":8,"author":[{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"full_name":"Calcabrini, Mariano","first_name":"Mariano","last_name":"Calcabrini"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"publication_status":"published","publisher":"Royal Society of Chemistry","department":[{"_id":"MaIb"}],"year":"2020","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council for scholarship support. M. C. has received funding from the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat \r\nAuto`noma de Barcelona Materials Science PhD program.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1039/D0TC02182B","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000581559100015"]},"month":"10"},{"publication_status":"submitted","title":"The habitable exoplanet observatory (HabEx) mission concept study final report","status":"public","year":"2020","_id":"14095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-21T10:10:21Z","date_updated":"2023-08-22T13:13:18Z","oa_version":"Preprint","author":[{"full_name":"Gaudi, B. Scott","last_name":"Gaudi","first_name":"B. Scott"},{"first_name":"Sara","last_name":"Seager","full_name":"Seager, Sara"},{"first_name":"Bertrand","last_name":"Mennesson","full_name":"Mennesson, Bertrand"},{"full_name":"Kiessling, Alina","first_name":"Alina","last_name":"Kiessling"},{"full_name":"Warfield, Keith","last_name":"Warfield","first_name":"Keith"},{"full_name":"Cahoy, Kerri","last_name":"Cahoy","first_name":"Kerri"},{"last_name":"Clarke","first_name":"John T.","full_name":"Clarke, John T."},{"full_name":"Shawn Domagal-Goldman, Shawn Domagal-Goldman","first_name":"Shawn Domagal-Goldman","last_name":"Shawn Domagal-Goldman"},{"full_name":"Feinberg, Lee","last_name":"Feinberg","first_name":"Lee"},{"last_name":"Guyon","first_name":"Olivier","full_name":"Guyon, Olivier"},{"last_name":"Kasdin","first_name":"Jeremy","full_name":"Kasdin, Jeremy"},{"full_name":"Mawet, Dimitri","last_name":"Mawet","first_name":"Dimitri"},{"last_name":"Plavchan","first_name":"Peter","full_name":"Plavchan, Peter"},{"full_name":"Robinson, Tyler","last_name":"Robinson","first_name":"Tyler"},{"last_name":"Rogers","first_name":"Leslie","full_name":"Rogers, Leslie"},{"first_name":"Paul","last_name":"Scowen","full_name":"Scowen, Paul"},{"last_name":"Somerville","first_name":"Rachel","full_name":"Somerville, Rachel"},{"first_name":"Karl","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Karl"},{"last_name":"Stark","first_name":"Christopher","full_name":"Stark, Christopher"},{"full_name":"Stern, Daniel","last_name":"Stern","first_name":"Daniel"},{"last_name":"Turnbull","first_name":"Margaret","full_name":"Turnbull, Margaret"},{"full_name":"Amini, Rashied","first_name":"Rashied","last_name":"Amini"},{"last_name":"Kuan","first_name":"Gary","full_name":"Kuan, Gary"},{"first_name":"Stefan","last_name":"Martin","full_name":"Martin, Stefan"},{"full_name":"Morgan, Rhonda","last_name":"Morgan","first_name":"Rhonda"},{"first_name":"David","last_name":"Redding","full_name":"Redding, David"},{"full_name":"Stahl, H. Philip","last_name":"Stahl","first_name":"H. Philip"},{"last_name":"Webb","first_name":"Ryan","full_name":"Webb, Ryan"},{"last_name":"Oscar Alvarez-Salazar","first_name":"Oscar Alvarez-Salazar","full_name":"Oscar Alvarez-Salazar, Oscar Alvarez-Salazar"},{"last_name":"Arnold","first_name":"William L.","full_name":"Arnold, William L."},{"first_name":"Manan","last_name":"Arya","full_name":"Arya, Manan"},{"full_name":"Balasubramanian, Bala","last_name":"Balasubramanian","first_name":"Bala"},{"last_name":"Baysinger","first_name":"Mike","full_name":"Baysinger, Mike"},{"full_name":"Bell, Ray","first_name":"Ray","last_name":"Bell"},{"full_name":"Below, Chris","first_name":"Chris","last_name":"Below"},{"first_name":"Jonathan","last_name":"Benson","full_name":"Benson, Jonathan"},{"full_name":"Blais, Lindsey","last_name":"Blais","first_name":"Lindsey"},{"first_name":"Jeff","last_name":"Booth","full_name":"Booth, Jeff"},{"last_name":"Bourgeois","first_name":"Robert","full_name":"Bourgeois, Robert"},{"last_name":"Bradford","first_name":"Case","full_name":"Bradford, Case"},{"last_name":"Brewer","first_name":"Alden","full_name":"Brewer, Alden"},{"full_name":"Brooks, Thomas","first_name":"Thomas","last_name":"Brooks"},{"first_name":"Eric","last_name":"Cady","full_name":"Cady, Eric"},{"first_name":"Mary","last_name":"Caldwell","full_name":"Caldwell, Mary"},{"full_name":"Calvet, Rob","last_name":"Calvet","first_name":"Rob"},{"first_name":"Steven","last_name":"Carr","full_name":"Carr, Steven"},{"full_name":"Chan, Derek","last_name":"Chan","first_name":"Derek"},{"first_name":"Velibor","last_name":"Cormarkovic","full_name":"Cormarkovic, Velibor"},{"full_name":"Coste, Keith","first_name":"Keith","last_name":"Coste"},{"last_name":"Cox","first_name":"Charlie","full_name":"Cox, Charlie"},{"full_name":"Danner, Rolf","last_name":"Danner","first_name":"Rolf"},{"first_name":"Jacqueline","last_name":"Davis","full_name":"Davis, Jacqueline"},{"full_name":"Dewell, Larry","last_name":"Dewell","first_name":"Larry"},{"full_name":"Dorsett, Lisa","last_name":"Dorsett","first_name":"Lisa"},{"first_name":"Daniel","last_name":"Dunn","full_name":"Dunn, Daniel"},{"full_name":"East, Matthew","first_name":"Matthew","last_name":"East"},{"full_name":"Effinger, Michael","last_name":"Effinger","first_name":"Michael"},{"first_name":"Ron","last_name":"Eng","full_name":"Eng, Ron"},{"full_name":"Freebury, Greg","last_name":"Freebury","first_name":"Greg"},{"last_name":"Garcia","first_name":"Jay","full_name":"Garcia, Jay"},{"full_name":"Gaskin, Jonathan","first_name":"Jonathan","last_name":"Gaskin"},{"full_name":"Greene, Suzan","first_name":"Suzan","last_name":"Greene"},{"full_name":"Hennessy, John","first_name":"John","last_name":"Hennessy"},{"full_name":"Hilgemann, Evan","last_name":"Hilgemann","first_name":"Evan"},{"full_name":"Hood, Brad","first_name":"Brad","last_name":"Hood"},{"last_name":"Holota","first_name":"Wolfgang","full_name":"Holota, Wolfgang"},{"full_name":"Howe, Scott","first_name":"Scott","last_name":"Howe"},{"full_name":"Huang, Pei","first_name":"Pei","last_name":"Huang"},{"full_name":"Hull, Tony","first_name":"Tony","last_name":"Hull"},{"last_name":"Hunt","first_name":"Ron","full_name":"Hunt, Ron"},{"last_name":"Hurd","first_name":"Kevin","full_name":"Hurd, Kevin"},{"full_name":"Johnson, Sandra","first_name":"Sandra","last_name":"Johnson"},{"last_name":"Kissil","first_name":"Andrew","full_name":"Kissil, Andrew"},{"full_name":"Knight, Brent","first_name":"Brent","last_name":"Knight"},{"first_name":"Daniel","last_name":"Kolenz","full_name":"Kolenz, Daniel"},{"first_name":"Oliver","last_name":"Kraus","full_name":"Kraus, Oliver"},{"full_name":"Krist, John","first_name":"John","last_name":"Krist"},{"full_name":"Li, Mary","last_name":"Li","first_name":"Mary"},{"full_name":"Lisman, Doug","last_name":"Lisman","first_name":"Doug"},{"first_name":"Milan","last_name":"Mandic","full_name":"Mandic, Milan"},{"last_name":"Mann","first_name":"John","full_name":"Mann, John"},{"full_name":"Marchen, Luis","first_name":"Luis","last_name":"Marchen"},{"first_name":"Colleen Marrese-Reading","last_name":"Colleen Marrese-Reading","full_name":"Colleen Marrese-Reading, Colleen Marrese-Reading"},{"first_name":"Jonathan","last_name":"McCready","full_name":"McCready, Jonathan"},{"full_name":"McGown, Jim","first_name":"Jim","last_name":"McGown"},{"full_name":"Missun, Jessica","first_name":"Jessica","last_name":"Missun"},{"last_name":"Miyaguchi","first_name":"Andrew","full_name":"Miyaguchi, Andrew"},{"full_name":"Moore, Bradley","first_name":"Bradley","last_name":"Moore"},{"first_name":"Bijan","last_name":"Nemati","full_name":"Nemati, Bijan"},{"full_name":"Nikzad, Shouleh","first_name":"Shouleh","last_name":"Nikzad"},{"full_name":"Nissen, Joel","first_name":"Joel","last_name":"Nissen"},{"full_name":"Novicki, Megan","first_name":"Megan","last_name":"Novicki"},{"full_name":"Perrine, Todd","last_name":"Perrine","first_name":"Todd"},{"full_name":"Pineda, Claudia","last_name":"Pineda","first_name":"Claudia"},{"full_name":"Polanco, Otto","last_name":"Polanco","first_name":"Otto"},{"last_name":"Putnam","first_name":"Dustin","full_name":"Putnam, Dustin"},{"first_name":"Atif","last_name":"Qureshi","full_name":"Qureshi, Atif"},{"full_name":"Richards, Michael","last_name":"Richards","first_name":"Michael"},{"last_name":"Riggs","first_name":"A. J. Eldorado","full_name":"Riggs, A. J. Eldorado"},{"full_name":"Rodgers, Michael","last_name":"Rodgers","first_name":"Michael"},{"full_name":"Rud, Mike","last_name":"Rud","first_name":"Mike"},{"full_name":"Saini, Navtej","last_name":"Saini","first_name":"Navtej"},{"full_name":"Scalisi, Dan","first_name":"Dan","last_name":"Scalisi"},{"first_name":"Dan","last_name":"Scharf","full_name":"Scharf, Dan"},{"first_name":"Kevin","last_name":"Schulz","full_name":"Schulz, Kevin"},{"first_name":"Gene","last_name":"Serabyn","full_name":"Serabyn, Gene"},{"first_name":"Norbert","last_name":"Sigrist","full_name":"Sigrist, Norbert"},{"full_name":"Sikkia, Glory","last_name":"Sikkia","first_name":"Glory"},{"first_name":"Andrew","last_name":"Singleton","full_name":"Singleton, Andrew"},{"full_name":"Shaklan, Stuart","first_name":"Stuart","last_name":"Shaklan"},{"last_name":"Smith","first_name":"Scott","full_name":"Smith, Scott"},{"last_name":"Southerd","first_name":"Bart","full_name":"Southerd, Bart"},{"first_name":"Mark","last_name":"Stahl","full_name":"Stahl, Mark"},{"last_name":"Steeves","first_name":"John","full_name":"Steeves, John"},{"last_name":"Sturges","first_name":"Brian","full_name":"Sturges, Brian"},{"first_name":"Chris","last_name":"Sullivan","full_name":"Sullivan, Chris"},{"first_name":"Hao","last_name":"Tang","full_name":"Tang, Hao"},{"full_name":"Taras, Neil","first_name":"Neil","last_name":"Taras"},{"first_name":"Jonathan","last_name":"Tesch","full_name":"Tesch, Jonathan"},{"first_name":"Melissa","last_name":"Therrell","full_name":"Therrell, Melissa"},{"full_name":"Tseng, Howard","first_name":"Howard","last_name":"Tseng"},{"full_name":"Valente, Marty","first_name":"Marty","last_name":"Valente"},{"first_name":"David Van","last_name":"Buren","full_name":"Buren, David Van"},{"full_name":"Villalvazo, Juan","last_name":"Villalvazo","first_name":"Juan"},{"full_name":"Warwick, Steve","last_name":"Warwick","first_name":"Steve"},{"first_name":"David","last_name":"Webb","full_name":"Webb, David"},{"full_name":"Westerhoff, Thomas","last_name":"Westerhoff","first_name":"Thomas"},{"full_name":"Wofford, Rush","first_name":"Rush","last_name":"Wofford"},{"last_name":"Wu","first_name":"Gordon","full_name":"Wu, Gordon"},{"full_name":"Woo, Jahning","last_name":"Woo","first_name":"Jahning"},{"full_name":"Wood, Milana","first_name":"Milana","last_name":"Wood"},{"full_name":"Ziemer, John","first_name":"John","last_name":"Ziemer"},{"first_name":"Giada","last_name":"Arney","full_name":"Arney, Giada"},{"first_name":"Jay","last_name":"Anderson","full_name":"Anderson, Jay"},{"full_name":"Jesús Maíz-Apellániz, Jesús Maíz-Apellániz","first_name":"Jesús Maíz-Apellániz","last_name":"Jesús Maíz-Apellániz"},{"last_name":"Bartlett","first_name":"James","full_name":"Bartlett, James"},{"full_name":"Belikov, Ruslan","first_name":"Ruslan","last_name":"Belikov"},{"last_name":"Bendek","first_name":"Eduardo","full_name":"Bendek, Eduardo"},{"first_name":"Brad","last_name":"Cenko","full_name":"Cenko, Brad"},{"last_name":"Douglas","first_name":"Ewan","full_name":"Douglas, Ewan"},{"last_name":"Dulz","first_name":"Shannon","full_name":"Dulz, Shannon"},{"full_name":"Evans, Chris","first_name":"Chris","last_name":"Evans"},{"full_name":"Faramaz, Virginie","last_name":"Faramaz","first_name":"Virginie"},{"last_name":"Feng","first_name":"Y. Katherina","full_name":"Feng, Y. Katherina"},{"full_name":"Ferguson, Harry","first_name":"Harry","last_name":"Ferguson"},{"last_name":"Follette","first_name":"Kate","full_name":"Follette, Kate"},{"first_name":"Saavik","last_name":"Ford","full_name":"Ford, Saavik"},{"last_name":"García","first_name":"Miriam","full_name":"García, Miriam"},{"first_name":"Marla","last_name":"Geha","full_name":"Geha, Marla"},{"full_name":"Gelino, Dawn","last_name":"Gelino","first_name":"Dawn"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter"},{"first_name":"Sergi","last_name":"Hildebrandt","full_name":"Hildebrandt, Sergi"},{"last_name":"Hu","first_name":"Renyu","full_name":"Hu, Renyu"},{"last_name":"Jahnke","first_name":"Knud","full_name":"Jahnke, Knud"},{"full_name":"Kennedy, Grant","first_name":"Grant","last_name":"Kennedy"},{"last_name":"Kreidberg","first_name":"Laura","full_name":"Kreidberg, Laura"},{"last_name":"Isella","first_name":"Andrea","full_name":"Isella, Andrea"},{"first_name":"Eric","last_name":"Lopez","full_name":"Lopez, Eric"},{"full_name":"Marchis, Franck","first_name":"Franck","last_name":"Marchis"},{"last_name":"Macri","first_name":"Lucas","full_name":"Macri, Lucas"},{"full_name":"Marley, Mark","first_name":"Mark","last_name":"Marley"},{"full_name":"Matzko, William","first_name":"William","last_name":"Matzko"},{"last_name":"Mazoyer","first_name":"Johan","full_name":"Mazoyer, Johan"},{"full_name":"McCandliss, Stephan","last_name":"McCandliss","first_name":"Stephan"},{"first_name":"Tiffany","last_name":"Meshkat","full_name":"Meshkat, Tiffany"},{"full_name":"Mordasini, Christoph","last_name":"Mordasini","first_name":"Christoph"},{"full_name":"Morris, Patrick","last_name":"Morris","first_name":"Patrick"},{"last_name":"Nielsen","first_name":"Eric","full_name":"Nielsen, Eric"},{"first_name":"Patrick","last_name":"Newman","full_name":"Newman, Patrick"},{"full_name":"Petigura, Erik","first_name":"Erik","last_name":"Petigura"},{"full_name":"Postman, Marc","first_name":"Marc","last_name":"Postman"},{"last_name":"Reines","first_name":"Amy","full_name":"Reines, Amy"},{"first_name":"Aki","last_name":"Roberge","full_name":"Roberge, Aki"},{"last_name":"Roederer","first_name":"Ian","full_name":"Roederer, Ian"},{"full_name":"Ruane, Garreth","last_name":"Ruane","first_name":"Garreth"},{"full_name":"Schwieterman, Edouard","first_name":"Edouard","last_name":"Schwieterman"},{"last_name":"Sirbu","first_name":"Dan","full_name":"Sirbu, Dan"},{"first_name":"Christopher","last_name":"Spalding","full_name":"Spalding, Christopher"},{"last_name":"Teplitz","first_name":"Harry","full_name":"Teplitz, Harry"},{"first_name":"Jason","last_name":"Tumlinson","full_name":"Tumlinson, Jason"},{"full_name":"Turner, Neal","first_name":"Neal","last_name":"Turner"},{"full_name":"Werk, Jessica","last_name":"Werk","first_name":"Jessica"},{"last_name":"Wofford","first_name":"Aida","full_name":"Wofford, Aida"},{"last_name":"Wyatt","first_name":"Mark","full_name":"Wyatt, Mark"},{"full_name":"Young, Amber","first_name":"Amber","last_name":"Young"},{"first_name":"Rob","last_name":"Zellem","full_name":"Zellem, Rob"}],"article_number":"2001.06683","type":"preprint","extern":"1","abstract":[{"lang":"eng","text":"The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument."}],"publication":"arXiv","oa":1,"external_id":{"arxiv":["2001.06683"]},"citation":{"chicago":"Gaudi, B. Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683.","short":"B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy, J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin, D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt, C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding, H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian, M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois, C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D. Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett, D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene, J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R. Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist, M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading, J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad, J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi, M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf, K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith, B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras, J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick, D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney, J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek, B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K. Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt, R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L. Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini, P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge, I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J. Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv (n.d.).","mla":"Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683.","ieee":"B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission concept study final report,” arXiv. .","apa":"Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy, K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683","ista":"Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv, 2001.06683.","ama":"Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683"},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2001.06683"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2001.06683","date_published":"2020-01-18T00:00:00Z","month":"01","day":"18","article_processing_charge":"No"},{"month":"11","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000591317200004"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1008402","language":[{"iso":"eng"}],"article_number":"e1008402","file_date_updated":"2020-11-18T07:26:10Z","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","author":[{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"last_name":"McAvoy","first_name":"Alex","full_name":"McAvoy, Alex"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"date_created":"2020-11-18T07:20:23Z","date_updated":"2023-08-22T12:49:18Z","volume":16,"scopus_import":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"day":"05","article_processing_charge":"No","has_accepted_license":"1","publication":"PLOS Computational Biology","citation":{"ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402.","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020)."},"article_type":"original","date_published":"2020-11-05T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"issue":"11","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The Moran process on 2-chromatic graphs","ddc":["000"],"status":"public","intvolume":" 16","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_PlosCompBio_Kaveh.pdf","creator":"dernst","content_type":"application/pdf","file_size":2498594,"file_id":"8768","relation":"main_file","success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","date_updated":"2020-11-18T07:26:10Z","date_created":"2020-11-18T07:26:10Z"}]},{"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.12325"}],"external_id":{"isi":["000661920400013"],"arxiv":["2006.12325"]},"language":[{"iso":"eng"}],"doi":"10.1109/MEMOCODE51338.2020.9314994","conference":{"name":"MEMOCODE: Conference on Formal Methods and Models for System Design","location":"Virtual Conference","start_date":"2020-12-02","end_date":"2020-12-04"},"publication_identifier":{"isbn":["9781728191485"]},"month":"12","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2020","date_updated":"2023-08-22T12:48:18Z","date_created":"2020-11-10T07:04:57Z","author":[{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Freire, Daniel","last_name":"Freire","first_name":"Daniel"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"article_number":"9314994","ec_funded":1,"citation":{"ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020.","apa":"Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.","ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994","chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994.","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994."},"publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","date_published":"2020-12-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04","status":"public","title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8750","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost."}]},{"date_published":"2020-12-01T00:00:00Z","page":"2257-2303","article_type":"original","citation":{"ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 2020;181(6):2257-2303. doi:10.1007/s10955-020-02663-4","ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303.","apa":"Maas, J., & Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02663-4","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” Journal of Statistical Physics, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:10.1007/s10955-020-02663-4.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02663-4."},"publication":"Journal of Statistical Physics","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"9087","relation":"main_file","success":1,"checksum":"bc2b63a90197b97cbc73eccada4639f5","date_updated":"2021-02-04T10:29:11Z","date_created":"2021-02-04T10:29:11Z","access_level":"open_access","file_name":"2020_JourStatPhysics_Maas.pdf","creator":"dernst","content_type":"application/pdf","file_size":753596}],"intvolume":" 181","status":"public","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","ddc":["510"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8758","issue":"6","abstract":[{"lang":"eng","text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s10955-020-02663-4","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2004.02831"],"isi":["000587107200002"]},"oa":1,"publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"month":"12","volume":181,"date_updated":"2023-08-22T13:24:27Z","date_created":"2020-11-15T23:01:18Z","author":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"},{"full_name":"Mielke, Alexander","first_name":"Alexander","last_name":"Mielke"}],"publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2020","acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","ec_funded":1,"file_date_updated":"2021-02-04T10:29:11Z"},{"article_processing_charge":"No","month":"09","day":"27","citation":{"ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"doi":"10.5281/ZENODO.4052882","date_published":"2020-09-27T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"publisher":"Zenodo","department":[{"_id":"JoFi"}],"title":"Surpassing the resistance quantum with a geometric superinductor","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13070","year":"2020","oa_version":"Published Version","date_updated":"2023-08-22T13:23:57Z","date_created":"2023-05-23T16:42:30Z","related_material":{"record":[{"id":"8755","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea"},{"first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}]},{"scopus_import":"1","day":"13","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Nature Communications","citation":{"ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020)."},"date_published":"2020-11-13T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"ddc":["570"],"status":"public","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","intvolume":" 11","_id":"8787","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"8798","relation":"main_file","success":1,"checksum":"485b7b6cf30198ba0ce126491a28f125","date_created":"2020-11-23T13:29:49Z","date_updated":"2020-11-23T13:29:49Z","access_level":"open_access","file_name":"2020_NatureComm_Nicolai.pdf","creator":"dernst","file_size":7035340,"content_type":"application/pdf"}],"oa_version":"Published Version","month":"11","publication_identifier":{"eissn":["20411723"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"external_id":{"pmid":["33188196"],"isi":["000594648000014"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19515-0","article_number":"5778","file_date_updated":"2020-11-23T13:29:49Z","ec_funded":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","year":"2020","pmid":1,"date_created":"2020-11-22T23:01:23Z","date_updated":"2023-08-22T13:26:26Z","volume":11,"author":[{"full_name":"Nicolai, Leo","first_name":"Leo","last_name":"Nicolai"},{"full_name":"Schiefelbein, Karin","last_name":"Schiefelbein","first_name":"Karin"},{"full_name":"Lipsky, Silvia","last_name":"Lipsky","first_name":"Silvia"},{"first_name":"Alexander","last_name":"Leunig","full_name":"Leunig, Alexander"},{"last_name":"Hoffknecht","first_name":"Marie","full_name":"Hoffknecht, Marie"},{"full_name":"Pekayvaz, Kami","last_name":"Pekayvaz","first_name":"Kami"},{"full_name":"Raude, Ben","last_name":"Raude","first_name":"Ben"},{"full_name":"Marx, Charlotte","last_name":"Marx","first_name":"Charlotte"},{"last_name":"Ehrlich","first_name":"Andreas","full_name":"Ehrlich, Andreas"},{"full_name":"Pircher, Joachim","first_name":"Joachim","last_name":"Pircher"},{"last_name":"Zhang","first_name":"Zhe","full_name":"Zhang, Zhe"},{"first_name":"Inas","last_name":"Saleh","full_name":"Saleh, Inas"},{"full_name":"Marel, Anna-Kristina","last_name":"Marel","first_name":"Anna-Kristina"},{"first_name":"Achim","last_name":"Löf","full_name":"Löf, Achim"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"full_name":"Pick, Robert","first_name":"Robert","last_name":"Pick"},{"full_name":"Rosenberger, Gerhild","first_name":"Gerhild","last_name":"Rosenberger"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"full_name":"Uhl, Bernd","last_name":"Uhl","first_name":"Bernd"},{"full_name":"Xia, Sheng","first_name":"Sheng","last_name":"Xia"},{"full_name":"Reichel, Christoph Andreas","last_name":"Reichel","first_name":"Christoph Andreas"},{"last_name":"Walzog","first_name":"Barbara","full_name":"Walzog, Barbara"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"full_name":"Bender, Markus","last_name":"Bender","first_name":"Markus"},{"last_name":"Li","first_name":"Rong","full_name":"Li, Rong"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]}},{"date_created":"2020-11-22T23:01:24Z","date_updated":"2023-08-22T13:25:45Z","volume":8,"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"},{"full_name":"Streipert, Sabrina","first_name":"Sabrina","last_name":"Streipert"},{"last_name":"Filar","first_name":"Jerzy","full_name":"Filar, Jerzy"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"KrCh"}],"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","year":"2020","file_date_updated":"2020-11-23T13:06:30Z","ec_funded":1,"article_number":"1945","language":[{"iso":"eng"}],"doi":"10.3390/math8111945","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000593962100001"]},"month":"11","publication_identifier":{"eissn":["22277390"]},"file":[{"file_id":"8797","relation":"main_file","success":1,"checksum":"61cfcc3b35760656ce7a9385a4ace5d2","date_updated":"2020-11-23T13:06:30Z","date_created":"2020-11-23T13:06:30Z","access_level":"open_access","file_name":"2020_Mathematics_Kleshnina.pdf","creator":"dernst","file_size":565191,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["000"],"status":"public","title":"Prioritised learning in snowdrift-type games","intvolume":" 8","_id":"8789","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2020-11-04T00:00:00Z","article_type":"original","publication":"Mathematics","citation":{"ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. Mathematics. 2020;8(11). doi:10.3390/math8111945","ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.","apa":"Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics, vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8111945."},"day":"04","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"ec_funded":1,"file_date_updated":"2020-08-24T12:53:15Z","related_material":{"record":[{"id":"8790","status":"public","relation":"later_version"}]},"author":[{"last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"last_name":"Potomkin","first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"}],"date_created":"2020-08-24T12:56:20Z","date_updated":"2023-08-22T13:27:32Z","year":"2020","department":[{"_id":"ToHe"}],"publication_status":"published","conference":{"start_date":"2020-09-20","location":"Virtual ","end_date":"2020-09-25","name":"EMSOFT: International Conference on Embedded Software"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1905.02458"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"type":"conference","file":[{"creator":"cschilli","file_size":696384,"content_type":"application/pdf","file_name":"2020EMSOFT.pdf","access_level":"open_access","date_created":"2020-08-24T12:53:15Z","date_updated":"2020-08-24T12:53:15Z","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75","file_id":"8288","relation":"main_file"}],"oa_version":"Preprint","_id":"8287","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["000"],"title":"Reachability analysis of linear hybrid systems via block decomposition","has_accepted_license":"1","article_processing_charge":"No","keyword":["reachability","hybrid systems","decomposition"],"date_published":"2020-01-01T00:00:00Z","citation":{"ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020."},"publication":"Proceedings of the International Conference on Embedded Software"},{"abstract":[{"lang":"eng","text":"We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically."}],"issue":"11","type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8788","title":"Precedence-aware automated competitive analysis of real-time scheduling","status":"public","intvolume":" 39","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","citation":{"ista":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 3981–3992.","ieee":"A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware automated competitive analysis of real-time scheduling,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 3981–3992, 2020.","apa":"Pavlogiannis, A., Schaumberger, N., Schmid, U., & Chatterjee, K. (2020). Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012803","ama":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):3981-3992. doi:10.1109/TCAD.2020.3012803","chicago":"Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012803.","mla":"Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:10.1109/TCAD.2020.3012803.","short":"A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992."},"article_type":"original","page":"3981-3992","author":[{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Schaumberger, Nico","last_name":"Schaumberger","first_name":"Nico"},{"first_name":"Ulrich","last_name":"Schmid","full_name":"Schmid, Ulrich"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"date_created":"2020-11-22T23:01:24Z","date_updated":"2023-08-22T13:27:05Z","volume":39,"year":"2020","acknowledgement":"This work was supported by the Austrian Science Foundation (FWF) under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented in the International Conference on Embedded Software 2020 and appears as part of the ESWEEK-TCAD special issue. ","publication_status":"published","publisher":"IEEE","department":[{"_id":"KrCh"}],"month":"11","publication_identifier":{"issn":["02780070"],"eissn":["19374151"]},"doi":"10.1109/TCAD.2020.3012803","language":[{"iso":"eng"}],"external_id":{"isi":["000587712700069"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}]},{"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8287"}]},"author":[{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"}],"volume":39,"date_updated":"2023-08-22T13:27:33Z","date_created":"2020-11-22T23:01:25Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","year":"2020","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"month":"11","doi":"10.1109/TCAD.2020.3012859","language":[{"iso":"eng"}],"external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.02458"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","issue":"11","abstract":[{"lang":"eng","text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks."}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8790","intvolume":" 39","title":"Reachability analysis of linear hybrid systems via block decomposition","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","citation":{"chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012859","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859"},"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","page":"4018-4029","article_type":"original"},{"scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Frontiers in Plant Science","citation":{"chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.586870.","short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870.","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., & Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.586870","ieee":"C. Nibau et al., “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870"},"date_published":"2020-11-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression.","lang":"eng"}],"ddc":["580"],"title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","status":"public","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8924","oa_version":"Published Version","file":[{"file_name":"2020_Frontiers_Nibau.pdf","access_level":"open_access","file_size":1833244,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8929","date_created":"2020-12-09T09:14:19Z","date_updated":"2020-12-09T09:14:19Z","checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","success":1}],"month":"11","publication_identifier":{"eissn":["1664-462X"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000591637000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2020.586870","article_number":"586870","file_date_updated":"2020-12-09T09:14:19Z","publication_status":"published","publisher":"Frontiers","department":[{"_id":"EvBe"}],"year":"2020","acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","date_created":"2020-12-06T23:01:14Z","date_updated":"2023-08-24T10:50:00Z","volume":11,"author":[{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"last_name":"Kargios","first_name":"Nestoras","full_name":"Kargios, Nestoras"},{"last_name":"Mallioura","first_name":"Areti","full_name":"Mallioura, Areti"},{"full_name":"Fernandez-Fuentes, Narcis","last_name":"Fernandez-Fuentes","first_name":"Narcis"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John H.","last_name":"Doonan","full_name":"Doonan, John H."}]},{"publication_identifier":{"eissn":["21555435"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1021/acscatal.0c03210","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000592978900031"]},"ec_funded":1,"volume":10,"date_updated":"2023-08-24T10:52:32Z","date_created":"2020-12-06T23:01:15Z","author":[{"full_name":"Irtem, Erdem","first_name":"Erdem","last_name":"Irtem"},{"full_name":"Arenas Esteban, Daniel","last_name":"Arenas Esteban","first_name":"Daniel"},{"full_name":"Duarte, Miguel","last_name":"Duarte","first_name":"Miguel"},{"full_name":"Choukroun, Daniel","first_name":"Daniel","last_name":"Choukroun"},{"first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bals","first_name":"Sara","full_name":"Bals, Sara"},{"full_name":"Breugelmans, Tom","last_name":"Breugelmans","first_name":"Tom"}],"publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"publication_status":"published","acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2020","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2020-11-20T00:00:00Z","page":"13468-13478","article_type":"original","citation":{"chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis. American Chemical Society, 2020. https://doi.org/10.1021/acscatal.0c03210.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:10.1021/acscatal.0c03210.","apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.0c03210","ieee":"E. Irtem et al., “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” ACS Catalysis, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 2020;10(22):13468-13478. doi:10.1021/acscatal.0c03210"},"publication":"ACS Catalysis","issue":"22","abstract":[{"text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 10","title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8926"},{"abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.","lang":"eng"}],"issue":"18","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8944","status":"public","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","intvolume":" 102","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","publication":"Physical Review B","citation":{"chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","ieee":"M. Zemlicka et al., “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” Physical Review B, vol. 102, no. 18. American Physical Society, 2020.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.102.180508","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 2020;102(18). doi:10.1103/PhysRevB.102.180508"},"article_type":"original","article_number":"180508","author":[{"last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"full_name":"Szabó, P.","last_name":"Szabó","first_name":"P."},{"full_name":"Samuely, T.","first_name":"T.","last_name":"Samuely"},{"full_name":"Kačmarčík, J.","first_name":"J.","last_name":"Kačmarčík"},{"last_name":"Neilinger","first_name":"P.","full_name":"Neilinger, P."},{"full_name":"Grajcar, M.","first_name":"M.","last_name":"Grajcar"},{"full_name":"Samuely, P.","first_name":"P.","last_name":"Samuely"}],"date_created":"2020-12-13T23:01:21Z","date_updated":"2023-08-24T10:53:36Z","volume":102,"year":"2020","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"month":"11","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"doi":"10.1103/PhysRevB.102.180508","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"oa":1,"external_id":{"arxiv":["2011.04329"],"isi":["000591509900003"]},"quality_controlled":"1","isi":1},{"volume":11,"date_updated":"2023-08-24T11:00:45Z","date_created":"2020-12-20T23:01:18Z","author":[{"last_name":"Rizzo","first_name":"Rossella","full_name":"Rizzo, Rossella"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"last_name":"Wang","first_name":"Jilin W.J.L.","full_name":"Wang, Jilin W.J.L."},{"first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch","last_name":"Ivanov"}],"publisher":"Frontiers","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","year":"2020","ec_funded":1,"file_date_updated":"2020-12-21T10:37:50Z","article_number":"558070","language":[{"iso":"eng"}],"doi":"10.3389/fphys.2020.558070","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"publication_identifier":{"eissn":["1664042X"]},"month":"11","file":[{"file_size":13380030,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_Frontiers_Rizzo.pdf","checksum":"ef9515b28c5619b7126c0f347958bcb3","success":1,"date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-21T10:37:50Z","relation":"main_file","file_id":"8961"}],"oa_version":"Published Version","intvolume":" 11","ddc":["570"],"title":"Network physiology of cortico–muscular interactions","status":"public","_id":"8955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies."}],"type":"journal_article","date_published":"2020-11-26T00:00:00Z","article_type":"original","citation":{"apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070."},"publication":"Frontiers in Physiology","has_accepted_license":"1","article_processing_charge":"No","day":"26","scopus_import":"1"}]