[{"type":"journal_article","pmid":1,"citation":{"ama":"Xue H, Zhang Y, Xiao G. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 2020;25(6):520-522. doi:10.1016/j.tplants.2020.04.001","ieee":"H. Xue, Y. Zhang, and G. Xiao, “Neo-gibberellin signaling: Guiding the next generation of the green revolution,” Trends in Plant Science, vol. 25, no. 6. Elsevier, pp. 520–522, 2020.","mla":"Xue, Huidan, et al. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” Trends in Plant Science, vol. 25, no. 6, Elsevier, 2020, pp. 520–22, doi:10.1016/j.tplants.2020.04.001.","apa":"Xue, H., Zhang, Y., & Xiao, G. (2020). Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2020.04.001","short":"H. Xue, Y. Zhang, G. Xiao, Trends in Plant Science 25 (2020) 520–522.","ista":"Xue H, Zhang Y, Xiao G. 2020. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 25(6), 520–522.","chicago":"Xue, Huidan, Yuzhou Zhang, and Guanghui Xiao. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” Trends in Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.tplants.2020.04.001."},"date_updated":"2023-08-21T06:16:01Z","date_published":"2020-06-01T00:00:00Z","month":"06","scopus_import":"1","doi":"10.1016/j.tplants.2020.04.001","article_type":"original","oa_version":"None","title":"Neo-gibberellin signaling: Guiding the next generation of the green revolution","intvolume":" 25","article_processing_charge":"No","publication":"Trends in Plant Science","year":"2020","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The agricultural green revolution spectacularly enhanced crop yield and lodging resistance with modified DELLA-mediated gibberellin signaling. However, this was achieved at the expense of reduced nitrogen-use efficiency (NUE). Recently, Wu et al. revealed novel gibberellin signaling that provides a blueprint for improving tillering and NUE in Green Revolution varieties (GRVs). "}],"_id":"7686","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Huidan","last_name":"Xue","full_name":"Xue, Huidan"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, Guanghui","last_name":"Xiao","first_name":"Guanghui"}],"external_id":{"pmid":["32407691"],"isi":["000533518400003"]},"publication_identifier":{"issn":["1360-1385"]},"volume":25,"day":"01","isi":1,"department":[{"_id":"JiFr"}],"quality_controlled":"1","issue":"6","page":"520-522","publisher":"Elsevier","date_created":"2020-04-26T22:00:46Z","status":"public"},{"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","article_processing_charge":"No","language":[{"iso":"ger"}],"year":"2020","intvolume":" 73","title":"(Core Trust) Seal your repository!","popular_science":"1","doi":"10.31263/voebm.v73i1.3491","article_type":"original","oa_version":"Published Version","file_date_updated":"2023-04-03T09:17:25Z","date_updated":"2024-02-27T13:41:03Z","citation":{"apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491.","ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491."},"has_accepted_license":"1","type":"journal_article","date_published":"2020-04-28T00:00:00Z","month":"04","ddc":["020"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","page":"46-59","file":[{"file_name":"2020_VOEB_Ernst.pdf","access_level":"open_access","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","date_created":"2020-06-17T10:50:13Z","file_size":579291,"content_type":"application/pdf","creator":"dernst","date_updated":"2023-04-03T09:17:25Z","relation":"main_file","file_id":"7970"}],"status":"public","date_created":"2020-04-28T08:37:38Z","day":"28","department":[{"_id":"E-Lib"}],"issue":"1","oa":1,"author":[{"first_name":"Doris","last_name":"Ernst","orcid":"0000-0002-2354-0195","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","full_name":"Ernst, Doris"},{"full_name":"Novotny, Gertraud","first_name":"Gertraud","last_name":"Novotny"},{"full_name":"Schönher, Eva Maria","last_name":"Schönher","first_name":"Eva Maria"}],"volume":73,"publication_identifier":{"issn":["1022-2588"]},"abstract":[{"text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.","lang":"eng"},{"text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich.","lang":"ger"}],"_id":"7687","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"article_processing_charge":"No","file":[{"relation":"main_file","file_id":"7786","file_size":5514403,"content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:48:02Z","creator":"gkatsaro","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","date_created":"2020-05-01T15:13:28Z","file_name":"DOI_ZeroFieldSplitting.zip","access_level":"open_access"}],"publisher":"Institute of Science and Technology Austria","year":"2020","date_created":"2020-05-01T15:14:46Z","status":"public","department":[{"_id":"GeKa"}],"day":"01","oa":1,"title":"Supplementary data for \"Zero field splitting of heavy-hole states in quantum dots\"","ec_funded":1,"doi":"10.15479/AT:ISTA:7689","contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","contributor_type":"contact_person"}],"author":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8203"}]},"file_date_updated":"2020-07-14T12:48:02Z","oa_version":"Published Version","project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"}],"_id":"7689","type":"research_data","has_accepted_license":"1","citation":{"ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","mla":"Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689.","ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689.","chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","short":"G. Katsaros, (2020)."},"abstract":[{"lang":"eng","text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n"}],"date_updated":"2024-02-21T12:44:02Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","date_published":"2020-05-01T00:00:00Z"},{"article_type":"original","doi":"10.1104/pp.20.00178","oa_version":"Preprint","citation":{"ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 2020;183(3):986-997. doi:10.1104/pp.20.00178","ieee":"J. Wang et al., “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” Plant Physiology, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020.","mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:10.1104/pp.20.00178.","apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00178","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997.","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00178."},"date_updated":"2023-09-05T12:20:02Z","pmid":1,"type":"journal_article","month":"07","date_published":"2020-07-01T00:00:00Z","scopus_import":"1","publication":"Plant Physiology","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2020","intvolume":" 183","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.13.948109"}],"title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","author":[{"full_name":"Wang, J","first_name":"J","last_name":"Wang"},{"last_name":"Mylle","first_name":"E","full_name":"Mylle, E"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"full_name":"Besbrugge, N","last_name":"Besbrugge","first_name":"N"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pleskot","first_name":"R","full_name":"Pleskot, R"},{"last_name":"van Damme","first_name":"D","full_name":"van Damme, D"}],"external_id":{"isi":["000550682000018"],"pmid":["32321842"]},"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"}],"volume":183,"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"abstract":[{"lang":"eng","text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex."}],"_id":"7695","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"American Society of Plant Biologists","page":"986-997","status":"public","date_created":"2020-04-29T15:23:00Z","isi":1,"day":"01","department":[{"_id":"JiFr"}],"quality_controlled":"1","issue":"3","oa":1},{"publisher":"Wiley","page":"1406-1416","file":[{"file_name":"2020_09_NewPhytologist_Zhang.pdf","access_level":"open_access","success":1,"checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","date_created":"2020-11-24T12:19:38Z","file_size":3643395,"content_type":"application/pdf","creator":"dernst","date_updated":"2020-11-24T12:19:38Z","relation":"main_file","file_id":"8799"}],"status":"public","date_created":"2020-04-30T08:43:29Z","isi":1,"day":"01","department":[{"_id":"JiFr"}],"quality_controlled":"1","oa":1,"issue":"5","external_id":{"isi":["000534092400001"],"pmid":["32350870"]},"author":[{"orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou"},{"first_name":"Corinna","orcid":"0000-0003-1618-2737","last_name":"Hartinger","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4","full_name":"Hartinger, Corinna"},{"last_name":"Wang","first_name":"Xiaojuan","full_name":"Wang, Xiaojuan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"volume":227,"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"abstract":[{"lang":"eng","text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants."}],"_id":"7697","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publication":"New Phytologist","article_processing_charge":"Yes (via OA deal)","year":"2020","language":[{"iso":"eng"}],"intvolume":" 227","title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","article_type":"original","doi":"10.1111/nph.16629","ec_funded":1,"oa_version":"Published Version","file_date_updated":"2020-11-24T12:19:38Z","citation":{"short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","apa":"Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629","chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16629.","ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:10.1111/nph.16629.","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” New Phytologist, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020."},"date_updated":"2023-09-05T15:46:04Z","has_accepted_license":"1","pmid":1,"type":"journal_article","date_published":"2020-09-01T00:00:00Z","month":"09","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1"},{"oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"volume":11,"article_type":"original","doi":"10.1038/s41467-020-15107-0","author":[{"first_name":"Jonathan","last_name":"Sulc","full_name":"Sulc, Jonathan"},{"full_name":"Mounier, Ninon","last_name":"Mounier","first_name":"Ninon"},{"full_name":"Günther, Felix","last_name":"Günther","first_name":"Felix"},{"last_name":"Winkler","first_name":"Thomas","full_name":"Winkler, Thomas"},{"full_name":"Wood, Andrew R.","first_name":"Andrew R.","last_name":"Wood"},{"full_name":"Frayling, Timothy M.","first_name":"Timothy M.","last_name":"Frayling"},{"full_name":"Heid, Iris M.","last_name":"Heid","first_name":"Iris M."},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Kutalik","first_name":"Zoltán","full_name":"Kutalik, Zoltán"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","date_published":"2020-03-20T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:14:59Z","abstract":[{"text":"The growing sample size of genome-wide association studies has facilitated the discovery of gene-environment interactions (GxE). Here we propose a maximum likelihood method to estimate the contribution of GxE to continuous traits taking into account all interacting environmental variables, without the need to measure any. Extensive simulations demonstrate that our method provides unbiased interaction estimates and excellent coverage. We also offer strategies to distinguish specific GxE from general scale effects. Applying our method to 32 traits in the UK Biobank reveals that while the genetic risk score (GRS) of 376 variants explains 5.2% of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless, this interaction holds for any variable with identical correlation to BMI as the GRS, hence may not be GRS-specific. Still, we observe that the global contribution of specific GRSxE to complex traits is substantial for nine obesity-related measures (including leg impedance and trunk fat-free mass).","lang":"eng"}],"citation":{"ama":"Sulc J, Mounier N, Günther F, et al. Quantification of the overall contribution of gene-environment interaction for obesity-related traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-15107-0","mla":"Sulc, Jonathan, et al. “Quantification of the Overall Contribution of Gene-Environment Interaction for Obesity-Related Traits.” Nature Communications, vol. 11, 1385, Springer Nature, 2020, doi:10.1038/s41467-020-15107-0.","ieee":"J. Sulc et al., “Quantification of the overall contribution of gene-environment interaction for obesity-related traits,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, Nature Communications 11 (2020).","apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2020). Quantification of the overall contribution of gene-environment interaction for obesity-related traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15107-0","chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Quantification of the Overall Contribution of Gene-Environment Interaction for Obesity-Related Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15107-0.","ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2020. Quantification of the overall contribution of gene-environment interaction for obesity-related traits. Nature Communications. 11, 1385."},"_id":"7707","article_number":"1385","date_created":"2020-04-30T10:39:33Z","status":"public","language":[{"iso":"eng"}],"year":"2020","extern":"1","article_processing_charge":"No","publication":"Nature Communications","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s41467-020-15107-0","open_access":"1"}],"quality_controlled":"1","title":"Quantification of the overall contribution of gene-environment interaction for obesity-related traits","intvolume":" 11","oa":1,"day":"20"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","date_published":"2020-02-27T00:00:00Z","_id":"7708","article_number":"10","type":"journal_article","citation":{"chicago":"Nabais, Marta F., Tian Lin, Beben Benyamin, Kelly L. Williams, Fleur C. Garton, Anna A. E. Vinkhuyzen, Futao Zhang, et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” Npj Genomic Medicine. Springer Nature, 2020. https://doi.org/10.1038/s41525-020-0118-3.","ista":"Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE, Zhang F, Vallerga CL, Restuadi R, Freydenzon A, Zwamborn RAJ, Hop PJ, Robinson MR, Gratten J, Visscher PM, Hannon E, Mill J, Brown MA, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Needham M, Veldink JH, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Yang J, Blair IP, McRae AF, Wray NR. 2020. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 5, 10.","short":"M.F. Nabais, T. Lin, B. Benyamin, K.L. Williams, F.C. Garton, A.A.E. Vinkhuyzen, F. Zhang, C.L. Vallerga, R. Restuadi, A. Freydenzon, R.A.J. Zwamborn, P.J. Hop, M.R. Robinson, J. Gratten, P.M. Visscher, E. Hannon, J. Mill, M.A. Brown, N.G. Laing, K.A. Mather, P.S. Sachdev, S.T. Ngo, F.J. Steyn, L. Wallace, A.K. Henders, M. Needham, J.H. Veldink, S. Mathers, G. Nicholson, D.B. Rowe, R.D. Henderson, P.A. McCombe, R. Pamphlett, J. Yang, I.P. Blair, A.F. McRae, N.R. Wray, Npj Genomic Medicine 5 (2020).","apa":"Nabais, M. F., Lin, T., Benyamin, B., Williams, K. L., Garton, F. C., Vinkhuyzen, A. A. E., … Wray, N. R. (2020). Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. Npj Genomic Medicine. Springer Nature. https://doi.org/10.1038/s41525-020-0118-3","mla":"Nabais, Marta F., et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” Npj Genomic Medicine, vol. 5, 10, Springer Nature, 2020, doi:10.1038/s41525-020-0118-3.","ieee":"M. F. Nabais et al., “Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis,” npj Genomic Medicine, vol. 5. Springer Nature, 2020.","ama":"Nabais MF, Lin T, Benyamin B, et al. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 2020;5. doi:10.1038/s41525-020-0118-3"},"date_updated":"2021-01-12T08:14:59Z","abstract":[{"text":"We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.","lang":"eng"}],"publication_identifier":{"issn":["2056-7944"]},"volume":5,"oa_version":"Published Version","doi":"10.1038/s41525-020-0118-3","article_type":"original","author":[{"full_name":"Nabais, Marta F.","last_name":"Nabais","first_name":"Marta F."},{"first_name":"Tian","last_name":"Lin","full_name":"Lin, Tian"},{"first_name":"Beben","last_name":"Benyamin","full_name":"Benyamin, Beben"},{"full_name":"Williams, Kelly L.","first_name":"Kelly L.","last_name":"Williams"},{"first_name":"Fleur C.","last_name":"Garton","full_name":"Garton, Fleur C."},{"last_name":"Vinkhuyzen","first_name":"Anna A. E.","full_name":"Vinkhuyzen, Anna A. E."},{"last_name":"Zhang","first_name":"Futao","full_name":"Zhang, Futao"},{"full_name":"Vallerga, Costanza L.","last_name":"Vallerga","first_name":"Costanza L."},{"first_name":"Restuadi","last_name":"Restuadi","full_name":"Restuadi, Restuadi"},{"full_name":"Freydenzon, Anna","first_name":"Anna","last_name":"Freydenzon"},{"first_name":"Ramona A. J.","last_name":"Zwamborn","full_name":"Zwamborn, Ramona A. J."},{"first_name":"Paul J.","last_name":"Hop","full_name":"Hop, Paul J."},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"last_name":"Gratten","first_name":"Jacob","full_name":"Gratten, Jacob"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."},{"full_name":"Hannon, Eilis","first_name":"Eilis","last_name":"Hannon"},{"last_name":"Mill","first_name":"Jonathan","full_name":"Mill, Jonathan"},{"first_name":"Matthew A.","last_name":"Brown","full_name":"Brown, Matthew A."},{"last_name":"Laing","first_name":"Nigel G.","full_name":"Laing, Nigel G."},{"last_name":"Mather","first_name":"Karen A.","full_name":"Mather, Karen A."},{"first_name":"Perminder S.","last_name":"Sachdev","full_name":"Sachdev, Perminder S."},{"full_name":"Ngo, Shyuan T.","last_name":"Ngo","first_name":"Shyuan T."},{"last_name":"Steyn","first_name":"Frederik J.","full_name":"Steyn, Frederik J."},{"last_name":"Wallace","first_name":"Leanne","full_name":"Wallace, Leanne"},{"full_name":"Henders, Anjali K.","first_name":"Anjali K.","last_name":"Henders"},{"last_name":"Needham","first_name":"Merrilee","full_name":"Needham, Merrilee"},{"first_name":"Jan H.","last_name":"Veldink","full_name":"Veldink, Jan H."},{"first_name":"Susan","last_name":"Mathers","full_name":"Mathers, Susan"},{"full_name":"Nicholson, Garth","first_name":"Garth","last_name":"Nicholson"},{"full_name":"Rowe, Dominic B.","last_name":"Rowe","first_name":"Dominic B."},{"last_name":"Henderson","first_name":"Robert D.","full_name":"Henderson, Robert D."},{"full_name":"McCombe, Pamela A.","last_name":"McCombe","first_name":"Pamela A."},{"full_name":"Pamphlett, Roger","last_name":"Pamphlett","first_name":"Roger"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"last_name":"Blair","first_name":"Ian P.","full_name":"Blair, Ian P."},{"last_name":"McRae","first_name":"Allan F.","full_name":"McRae, Allan F."},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."}],"oa":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41525-020-0118-3"}],"title":"Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis","intvolume":" 5","day":"27","year":"2020","language":[{"iso":"eng"}],"date_created":"2020-04-30T10:39:54Z","status":"public","publication":"npj Genomic Medicine","article_processing_charge":"No","publisher":"Springer Nature","extern":"1"},{"title":"Self-assembly-based posttranslational protein oscillators","intvolume":" 6","language":[{"iso":"eng"}],"year":"2020","extern":"1","article_processing_charge":"No","publication":"Science Advances","ddc":["570"],"date_published":"2020-12-16T00:00:00Z","month":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","citation":{"ama":"Kimchi O, Goodrich CP, Courbet A, et al. Self-assembly-based posttranslational protein oscillators. Science Advances. 2020;6(51). doi:10.1126/sciadv.abc1939","mla":"Kimchi, Ofer, et al. “Self-Assembly-Based Posttranslational Protein Oscillators.” Science Advances, vol. 6, no. 51, eabc1939, 2020, doi:10.1126/sciadv.abc1939.","ieee":"O. Kimchi et al., “Self-assembly-based posttranslational protein oscillators,” Science Advances, vol. 6, no. 51. 2020.","short":"O. Kimchi, C.P. Goodrich, A. Courbet, A.I. Curatolo, N.B. Woodall, D. Baker, M.P. Brenner, Science Advances 6 (2020).","apa":"Kimchi, O., Goodrich, C. P., Courbet, A., Curatolo, A. I., Woodall, N. B., Baker, D., & Brenner, M. P. (2020). Self-assembly-based posttranslational protein oscillators. Science Advances. https://doi.org/10.1126/sciadv.abc1939","chicago":"Kimchi, Ofer, Carl Peter Goodrich, Alexis Courbet, Agnese I. Curatolo, Nicholas B. Woodall, David Baker, and Michael P. Brenner. “Self-Assembly-Based Posttranslational Protein Oscillators.” Science Advances, 2020. https://doi.org/10.1126/sciadv.abc1939.","ista":"Kimchi O, Goodrich CP, Courbet A, Curatolo AI, Woodall NB, Baker D, Brenner MP. 2020. Self-assembly-based posttranslational protein oscillators. Science Advances. 6(51), eabc1939."},"date_updated":"2021-04-12T08:35:19Z","has_accepted_license":"1","article_number":"eabc1939","oa_version":"Published Version","file_date_updated":"2021-04-12T08:33:23Z","doi":"10.1126/sciadv.abc1939","article_type":"original","quality_controlled":"1","oa":1,"issue":"51","day":"16","date_created":"2020-04-30T12:07:55Z","status":"public","file":[{"file_size":1259758,"content_type":"application/pdf","creator":"dernst","date_updated":"2021-04-12T08:33:23Z","relation":"main_file","file_id":"9320","file_name":"2020_ScienceAdv_Kimchi.pdf","access_level":"open_access","success":1,"checksum":"eb6d950b6a68ddc4a2fb31ec80a2a1bd","date_created":"2021-04-12T08:33:23Z"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems."}],"_id":"7778","volume":6,"author":[{"full_name":"Kimchi, Ofer","last_name":"Kimchi","first_name":"Ofer"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Courbet","first_name":"Alexis","full_name":"Courbet, Alexis"},{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"full_name":"Woodall, Nicholas B.","first_name":"Nicholas B.","last_name":"Woodall"},{"first_name":"David","last_name":"Baker","full_name":"Baker, David"},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."}]},{"_id":"7788","abstract":[{"text":"Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids.","lang":"eng"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Adjobo-Hermans","first_name":"Merel J.W.","full_name":"Adjobo-Hermans, Merel J.W."},{"first_name":"Ria","last_name":"De Haas","full_name":"De Haas, Ria"},{"first_name":"Peter H.G.M.","last_name":"Willems","full_name":"Willems, Peter H.G.M."},{"last_name":"Wojtala","first_name":"Aleksandra","full_name":"Wojtala, Aleksandra"},{"last_name":"Van Emst-De Vries","first_name":"Sjenet E.","full_name":"Van Emst-De Vries, Sjenet E."},{"full_name":"Wagenaars, Jori A.","last_name":"Wagenaars","first_name":"Jori A."},{"first_name":"Mariel","last_name":"Van Den Brand","full_name":"Van Den Brand, Mariel"},{"last_name":"Rodenburg","first_name":"Richard J.","full_name":"Rodenburg, Richard J."},{"first_name":"Jan A.M.","last_name":"Smeitink","full_name":"Smeitink, Jan A.M."},{"full_name":"Nijtmans, Leo G.","last_name":"Nijtmans","first_name":"Leo G."},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wieckowski","first_name":"Mariusz R.","full_name":"Wieckowski, Mariusz R."},{"full_name":"Koopman, Werner J.H.","last_name":"Koopman","first_name":"Werner J.H."}],"external_id":{"isi":["000540842000012"],"pmid":["32335026"]},"publication_identifier":{"eissn":["18792650"],"issn":["00052728"]},"volume":1861,"department":[{"_id":"LeSa"}],"day":"01","isi":1,"issue":"8","oa":1,"quality_controlled":"1","file":[{"access_level":"open_access","file_name":"2020_BBA_Adjobo_Hermans.pdf","date_created":"2020-05-04T12:25:19Z","checksum":"a9b152381307cf45fe266a8dc5640388","date_updated":"2020-07-14T12:48:03Z","creator":"dernst","content_type":"application/pdf","file_size":3826792,"file_id":"7798","relation":"main_file"}],"publisher":"Elsevier","date_created":"2020-05-03T22:00:47Z","status":"public","article_number":"148213","pmid":1,"type":"journal_article","date_updated":"2023-08-21T06:19:18Z","has_accepted_license":"1","citation":{"ista":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213.","chicago":"Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand, et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213.","apa":"Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A., Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213","short":"M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink, L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica Acta - Bioenergetics 1861 (2020).","ieee":"M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8. Elsevier, 2020.","mla":"Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213, Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.","ama":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8). doi:10.1016/j.bbabio.2020.148213"},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2020-08-01T00:00:00Z","month":"08","doi":"10.1016/j.bbabio.2020.148213","article_type":"original","file_date_updated":"2020-07-14T12:48:03Z","oa_version":"Published Version","title":"NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2","intvolume":" 1861","article_processing_charge":"No","publication":"Biochimica et Biophysica Acta - Bioenergetics","language":[{"iso":"eng"}],"year":"2020"},{"date_created":"2020-05-03T22:00:48Z","status":"public","publisher":"Elsevier","page":"604-620.e22","file":[{"file_id":"7795","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf","file_size":17992888,"date_created":"2020-05-04T10:20:55Z","checksum":"e2114902f4e9d75a752e9efb5ae06011","access_level":"open_access","file_name":"2020_Cell_Dekoninck.pdf"}],"quality_controlled":"1","issue":"3","oa":1,"day":"30","isi":1,"department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"volume":181,"author":[{"last_name":"Dekoninck","first_name":"Sophie","full_name":"Dekoninck, Sophie"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sifrim, Alejandro","first_name":"Alejandro","last_name":"Sifrim"},{"full_name":"Miroshnikova, Yekaterina A.","first_name":"Yekaterina A.","last_name":"Miroshnikova"},{"first_name":"Mariaceleste","last_name":"Aragona","full_name":"Aragona, Mariaceleste"},{"first_name":"Milan","last_name":"Malfait","full_name":"Malfait, Milan"},{"last_name":"Gargouri","first_name":"Souhir","full_name":"Gargouri, Souhir"},{"last_name":"De Neunheuser","first_name":"Charlotte","full_name":"De Neunheuser, Charlotte"},{"full_name":"Dubois, Christine","first_name":"Christine","last_name":"Dubois"},{"full_name":"Voet, Thierry","last_name":"Voet","first_name":"Thierry"},{"last_name":"Wickström","first_name":"Sara A.","full_name":"Wickström, Sara A."},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"first_name":"Cédric","last_name":"Blanpain","full_name":"Blanpain, Cédric"}],"external_id":{"pmid":["32259486"],"isi":["000530708400016"]},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues."}],"_id":"7789","year":"2020","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"Cell","title":"Defining the design principles of skin epidermis postnatal growth","intvolume":" 181","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z","article_type":"original","doi":"10.1016/j.cell.2020.03.015","ddc":["570"],"date_published":"2020-04-30T00:00:00Z","month":"04","scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"pmid":1,"type":"journal_article","date_updated":"2023-08-21T06:17:43Z","citation":{"ista":"Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22.","chicago":"Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015.","apa":"Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015","short":"S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22.","ieee":"S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020.","mla":"Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015.","ama":"Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015"},"has_accepted_license":"1"},{"article_processing_charge":"No","publication":"Forum of Mathematics, Sigma","year":"2020","language":[{"iso":"eng"}],"intvolume":" 8","title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","related_material":{"record":[{"relation":"earlier_version","id":"7524","status":"public"}]},"article_type":"original","doi":"10.1017/fms.2020.17","ec_funded":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z","has_accepted_license":"1","date_updated":"2023-08-21T06:18:49Z","citation":{"apa":"Deuchert, A., Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2020.17","short":"A. Deuchert, S. Mayer, R. Seiringer, Forum of Mathematics, Sigma 8 (2020).","ista":"Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20.","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma. Cambridge University Press, 2020. https://doi.org/10.1017/fms.2020.17.","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 2020;8. doi:10.1017/fms.2020.17","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” Forum of Mathematics, Sigma, vol. 8. Cambridge University Press, 2020.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma, vol. 8, e20, Cambridge University Press, 2020, doi:10.1017/fms.2020.17."},"type":"journal_article","article_number":"e20","month":"03","date_published":"2020-03-14T00:00:00Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","file":[{"date_updated":"2020-07-14T12:48:03Z","creator":"dernst","content_type":"application/pdf","file_size":692530,"file_id":"7797","relation":"main_file","access_level":"open_access","file_name":"2020_ForumMath_Deuchert.pdf","date_created":"2020-05-04T12:02:41Z","checksum":"8a64da99d107686997876d7cad8cfe1e"}],"publisher":"Cambridge University Press","status":"public","date_created":"2020-05-03T22:00:48Z","isi":1,"day":"14","department":[{"_id":"RoSe"}],"quality_controlled":"1","arxiv":1,"oa":1,"author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"external_id":{"isi":["000527342000001"],"arxiv":["1910.03372"]},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"volume":8,"publication_identifier":{"eissn":["20505094"]},"abstract":[{"text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .","lang":"eng"}],"_id":"7790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published"},{"oa_version":"None","article_type":"original","doi":"10.1038/s41563-020-0665-0","date_published":"2020-09-01T00:00:00Z","month":"09","scopus_import":"1","pmid":1,"type":"journal_article","citation":{"apa":"Taboada-Gutiérrez, J., Álvarez-Pérez, G., Duan, J., Ma, W., Crowley, K., Prieto Gonzalez, I., … Alonso-González, P. (2020). Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-020-0665-0","short":"J. Taboada-Gutiérrez, G. Álvarez-Pérez, J. Duan, W. Ma, K. Crowley, I. Prieto Gonzalez, A. Bylinkin, M. Autore, H. Volkova, K. Kimura, T. Kimura, M.H. Berger, S. Li, Q. Bao, X.P.A. Gao, I. Errea, A.Y. Nikitin, R. Hillenbrand, J. Martín-Sánchez, P. Alonso-González, Nature Materials 19 (2020) 964–968.","ista":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, Ma W, Crowley K, Prieto Gonzalez I, Bylinkin A, Autore M, Volkova H, Kimura K, Kimura T, Berger MH, Li S, Bao Q, Gao XPA, Errea I, Nikitin AY, Hillenbrand R, Martín-Sánchez J, Alonso-González P. 2020. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. 19, 964–968.","chicago":"Taboada-Gutiérrez, Javier, Gonzalo Álvarez-Pérez, Jiahua Duan, Weiliang Ma, Kyle Crowley, Ivan Prieto Gonzalez, Andrei Bylinkin, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” Nature Materials. Springer Nature, 2020. https://doi.org/10.1038/s41563-020-0665-0.","ama":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, et al. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. 2020;19:964–968. doi:10.1038/s41563-020-0665-0","ieee":"J. Taboada-Gutiérrez et al., “Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation,” Nature Materials, vol. 19. Springer Nature, pp. 964–968, 2020.","mla":"Taboada-Gutiérrez, Javier, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” Nature Materials, vol. 19, Springer Nature, 2020, pp. 964–968, doi:10.1038/s41563-020-0665-0."},"date_updated":"2023-08-21T06:18:20Z","year":"2020","language":[{"iso":"eng"}],"publication":"Nature Materials","article_processing_charge":"No","title":"Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation","intvolume":" 19","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the Government of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA-20-PF-BP19-053, respectively). J.M.-S. acknowledges finantial support from the Clarín Programme from the Government of the Principality of Asturias and a Marie Curie-COFUND grant (PA-18-ACB17-29) and the Ramón y Cajal Program from the Government of Spain (RYC2018-026196-I). K.C., X.P.A.G., H.V. and M.H.B. acknowledge the Air Force Office of Scientific Research (AFOSR) grant no. FA 9550-18-1-0030 for funding support. I.E. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness (grant no. FIS2016-76617-P). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT2017-88358-C3-3-R) and the Basque Government (grant no. IT1164-19). Q.B. acknowledges the support from Australian Research Council (grant nos. FT150100450, IH150100006 and CE170100039). R.H. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (national project RTI2018-094830-B-100 and the Project MDM-2016-0618 of the María de Maeztu Units of Excellence Program) and the Basque Goverment (grant no. IT1164-19). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA.","publication_identifier":{"eissn":["14764660"],"issn":["14761122"]},"volume":19,"author":[{"last_name":"Taboada-Gutiérrez","first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"full_name":"Crowley, Kyle","last_name":"Crowley","first_name":"Kyle"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Bylinkin","first_name":"Andrei","full_name":"Bylinkin, Andrei"},{"last_name":"Autore","first_name":"Marta","full_name":"Autore, Marta"},{"full_name":"Volkova, Halyna","first_name":"Halyna","last_name":"Volkova"},{"first_name":"Kenta","last_name":"Kimura","full_name":"Kimura, Kenta"},{"full_name":"Kimura, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Kimura"},{"first_name":"M. H.","last_name":"Berger","full_name":"Berger, M. H."},{"full_name":"Li, Shaojuan","last_name":"Li","first_name":"Shaojuan"},{"full_name":"Bao, Qiaoliang","last_name":"Bao","first_name":"Qiaoliang"},{"last_name":"Gao","first_name":"Xuan P.A.","full_name":"Gao, Xuan P.A."},{"last_name":"Errea","first_name":"Ion","full_name":"Errea, Ion"},{"last_name":"Nikitin","first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y."},{"last_name":"Hillenbrand","first_name":"Rainer","full_name":"Hillenbrand, Rainer"},{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"external_id":{"pmid":["32284598"],"isi":["000526218500004"]},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Phonon polaritons—light coupled to lattice vibrations—in polar van der Waals crystals are promising candidates for controlling the flow of energy on the nanoscale due to their strong field confinement, anisotropic propagation and ultra-long lifetime in the picosecond range1,2,3,4,5. However, the lack of tunability of their narrow and material-specific spectral range—the Reststrahlen band—severely limits their technological implementation. Here, we demonstrate that intercalation of Na atoms in the van der Waals semiconductor α-V2O5 enables a broad spectral shift of Reststrahlen bands, and that the phonon polaritons excited show ultra-low losses (lifetime of 4 ± 1 ps), similar to phonon polaritons in a non-intercalated crystal (lifetime of 6 ± 1 ps). We expect our intercalation method to be applicable to other van der Waals crystals, opening the door for the use of phonon polaritons in broad spectral bands in the mid-infrared domain.","lang":"eng"}],"_id":"7792","date_created":"2020-05-03T22:00:49Z","status":"public","publisher":"Springer Nature","page":"964–968","quality_controlled":"1","day":"01","isi":1,"department":[{"_id":"NanoFab"}]},{"language":[{"iso":"eng"}],"year":"2020","article_processing_charge":"No","publication":"eLife","intvolume":" 9","title":"Direct ETTIN-auxin interaction controls chromatin states in gynoecium development","file_date_updated":"2020-07-14T12:48:03Z","oa_version":"Published Version","doi":"10.7554/elife.51787","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","month":"04","date_published":"2020-04-08T00:00:00Z","ddc":["580"],"article_number":"e51787","date_updated":"2023-08-21T06:17:12Z","has_accepted_license":"1","citation":{"apa":"Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51787","short":"A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020).","ista":"Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787.","chicago":"Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51787.","ama":"Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 2020;9. doi:10.7554/elife.51787","ieee":"A. Kuhn et al., “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife, vol. 9, e51787, eLife Sciences Publications, 2020, doi:10.7554/elife.51787."},"pmid":1,"type":"journal_article","status":"public","date_created":"2020-05-04T08:50:47Z","publisher":"eLife Sciences Publications","file":[{"relation":"main_file","file_id":"7794","file_size":2893082,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","creator":"dernst","checksum":"15d740de1a741fdcc6ec128c48eed017","date_created":"2020-05-04T09:06:43Z","file_name":"2020_eLife_Kuhn.pdf","access_level":"open_access"}],"oa":1,"quality_controlled":"1","department":[{"_id":"JiFr"}],"isi":1,"day":"08","volume":9,"publication_identifier":{"issn":["2050-084X"]},"author":[{"full_name":"Kuhn, André","first_name":"André","last_name":"Kuhn"},{"full_name":"Ramans Harborough, Sigurd","last_name":"Ramans Harborough","first_name":"Sigurd"},{"last_name":"McLaughlin","first_name":"Heather M","full_name":"McLaughlin, Heather M"},{"full_name":"Natarajan, Bhavani","first_name":"Bhavani","last_name":"Natarajan"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"first_name":"Stefan","last_name":"Kepinski","full_name":"Kepinski, Stefan"},{"full_name":"Østergaard, Lars","first_name":"Lars","last_name":"Østergaard"}],"external_id":{"isi":["000527752200001"],"pmid":["32267233"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","_id":"7793","abstract":[{"text":"Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner.","lang":"eng"}]},{"day":"11","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"oa":1,"file":[{"access_level":"open_access","file_name":"2020.01.10.902064v1.full.pdf","date_created":"2020-05-05T14:31:19Z","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","date_updated":"2020-07-14T12:48:03Z","creator":"rsix","content_type":"application/pdf","file_size":2931370,"file_id":"7801","relation":"main_file"}],"publisher":"Cold Spring Harbor Laboratory","status":"public","date_created":"2020-05-05T14:31:33Z","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.","lang":"eng"}],"_id":"7800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"first_name":"Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"orcid":"0000-0003-1843-3173","last_name":"Basilico","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","first_name":"Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"}],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","publication":"bioRxiv","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2020","acknowledged_ssus":[{"_id":"PreCl"}],"date_updated":"2024-09-10T12:04:26Z","citation":{"apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064 ","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.).","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, 10.1101/2020.01.10.902064 .","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 .","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. doi:10.1101/2020.01.10.902064 ","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 ."},"has_accepted_license":"1","type":"preprint","month":"01","date_published":"2020-01-11T00:00:00Z","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"related_material":{"record":[{"relation":"dissertation_contains","id":"8620","status":"public"},{"status":"public","id":"9429","relation":"later_version"}]},"doi":"10.1101/2020.01.10.902064 ","oa_version":"Preprint","file_date_updated":"2020-07-14T12:48:03Z"},{"author":[{"first_name":"Artur","last_name":"Czumaj","orcid":"0000-0002-5646-9524","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","orcid":"0000-0002-5646-9524","last_name":"Davies"},{"full_name":"Parter, Merav","first_name":"Merav","last_name":"Parter"}],"external_id":{"arxiv":["1912.05390"],"isi":["000744436200015"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17].","lang":"eng"}],"_id":"7802","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","page":"175-185","date_created":"2020-05-06T08:53:34Z","status":"public","day":"01","isi":1,"department":[{"_id":"DaAl"}],"quality_controlled":"1","issue":"7","oa":1,"arxiv":1,"conference":{"location":"Virtual Event, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2020-07-15","end_date":"2020-07-17"},"doi":"10.1145/3350755.3400282","related_material":{"record":[{"relation":"later_version","id":"9541","status":"public"}]},"ec_funded":1,"oa_version":"Preprint","type":"conference","citation":{"apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282."},"date_updated":"2024-02-28T12:53:09Z","month":"07","date_published":"2020-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","year":"2020","language":[{"iso":"eng"}],"title":"Graph sparsification for derandomizing massively parallel computation with low space","main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}]},{"date_created":"2020-05-06T09:02:14Z","status":"public","page":"309-318","file":[{"file_id":"8624","relation":"main_file","date_updated":"2020-10-08T08:17:36Z","creator":"pdavies","content_type":"application/pdf","file_size":520051,"date_created":"2020-10-08T08:17:36Z","checksum":"46fe4fc58a64eb04068115573f631d4c","success":1,"access_level":"open_access","file_name":"ColoringArxiv.pdf"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"arxiv":1,"day":"01","department":[{"_id":"DaAl"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"author":[{"first_name":"Artur","orcid":"0000-0002-5646-9524","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524","last_name":"Davies","first_name":"Peter","full_name":"Davies, Peter"},{"full_name":"Parter, Merav","first_name":"Merav","last_name":"Parter"}],"external_id":{"arxiv":["2009.06043"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We settle the complexity of the (Δ+1)-coloring and (Δ+1)-list coloring problems in the CONGESTED CLIQUE model by presenting a simple deterministic algorithm for both problems running in a constant number of rounds. This matches the complexity of the recent breakthrough randomized constant-round (Δ+1)-list coloring algorithm due to Chang et al. (PODC'19), and significantly improves upon the state-of-the-art O(logΔ)-round deterministic (Δ+1)-coloring bound of Parter (ICALP'18).\r\nA remarkable property of our algorithm is its simplicity. Whereas the state-of-the-art randomized algorithms for this problem are based on the quite involved local coloring algorithm of Chang et al. (STOC'18), our algorithm can be described in just a few lines. At a high level, it applies a careful derandomization of a recursive procedure which partitions the nodes and their respective palettes into separate bins. We show that after O(1) recursion steps, the remaining uncolored subgraph within each bin has linear size, and thus can be solved locally by collecting it to a single node. This algorithm can also be implemented in the Massively Parallel Computation (MPC) model provided that each machine has linear (in n, the number of nodes in the input graph) space.\r\nWe also show an extension of our algorithm to the MPC regime in which machines have sublinear space: we present the first deterministic (Δ+1)-list coloring algorithm designed for sublinear-space MPC, which runs in O(logΔ+loglogn) rounds.","lang":"eng"}],"_id":"7803","language":[{"iso":"eng"}],"year":"2020","publication":"Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing","article_processing_charge":"No","title":"Simple, deterministic, constant-round coloring in the congested clique","oa_version":"Submitted Version","file_date_updated":"2020-10-08T08:17:36Z","doi":"10.1145/3382734.3405751","conference":{"start_date":"2020-08-03","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2020-08-07","location":"Salerno, Italy"},"ec_funded":1,"ddc":["000"],"month":"07","date_published":"2020-07-01T00:00:00Z","type":"conference","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Simple, Deterministic, Constant-Round Coloring in the Congested Clique.” In Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, 309–18. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405751.","ista":"Czumaj A, Davies P, Parter M. 2020. Simple, deterministic, constant-round coloring in the congested clique. Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 309–318.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 309–318.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Simple, deterministic, constant-round coloring in the congested clique. In Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing (pp. 309–318). Salerno, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405751","mla":"Czumaj, Artur, et al. “Simple, Deterministic, Constant-Round Coloring in the Congested Clique.” Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 309–18, doi:10.1145/3382734.3405751.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Simple, deterministic, constant-round coloring in the congested clique,” in Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Salerno, Italy, 2020, pp. 309–318.","ama":"Czumaj A, Davies P, Parter M. Simple, deterministic, constant-round coloring in the congested clique. In: Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:309-318. doi:10.1145/3382734.3405751"},"has_accepted_license":"1","date_updated":"2021-01-12T08:15:37Z"},{"date_created":"2020-05-10T22:00:47Z","status":"public","file":[{"date_created":"2020-05-11T10:36:33Z","checksum":"dce367abf2c1a1d15f58fe6f7de82893","access_level":"open_access","file_name":"2020_NatureComm_Flynn.pdf","file_id":"7817","relation":"main_file","content_type":"application/pdf","file_size":4609120,"creator":"dernst","date_updated":"2020-07-14T12:48:03Z"}],"publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"29","isi":1,"department":[{"_id":"MaDe"}],"publication_identifier":{"eissn":["20411723"]},"volume":11,"external_id":{"isi":["000531855500029"]},"author":[{"last_name":"Flynn","first_name":"Sean M.","full_name":"Flynn, Sean M."},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"full_name":"Artan, Murat","first_name":"Murat","orcid":"0000-0001-8945-6992","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"full_name":"Barratt, Stephen","last_name":"Barratt","first_name":"Stephen"},{"full_name":"Crisp, Alastair","first_name":"Alastair","last_name":"Crisp"},{"last_name":"Nelson","first_name":"Geoffrey M.","full_name":"Nelson, Geoffrey M."},{"last_name":"Peak-Chew","first_name":"Sew Yeu","full_name":"Peak-Chew, Sew Yeu"},{"full_name":"Begum, Farida","last_name":"Begum","first_name":"Farida"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"full_name":"De Bono, Mario","first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.","lang":"eng"}],"_id":"7804","language":[{"iso":"eng"}],"year":"2020","publication":"Nature Communications","article_processing_charge":"No","title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","intvolume":" 11","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z","article_type":"original","doi":"10.1038/s41467-020-15872-y","ddc":["570"],"month":"04","date_published":"2020-04-29T00:00:00Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_updated":"2023-08-21T06:21:14Z","has_accepted_license":"1","citation":{"chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15872-y.","ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099.","short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15872-y","mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications, vol. 11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y.","ieee":"S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 2020;11. doi:10.1038/s41467-020-15872-y"},"article_number":"2099"},{"date_updated":"2023-08-21T06:21:56Z","has_accepted_license":"1","citation":{"short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15895-5","chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.","ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-15895-5","mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications, vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5.","ieee":"A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” Nature Communications, vol. 11. Springer Nature, 2020."},"pmid":1,"type":"journal_article","article_number":"2170","month":"05","date_published":"2020-05-01T00:00:00Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","article_type":"original","doi":"10.1038/s41467-020-15895-5","ec_funded":1,"oa_version":"Published Version","file_date_updated":"2020-10-06T07:47:53Z","acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","intvolume":" 11","title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","publication":"Nature Communications","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2020","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens."}],"_id":"7805","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cuesta, Candela","last_name":"Cuesta","orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","last_name":"Ötvös","first_name":"Krisztina","full_name":"Ötvös, Krisztina"},{"full_name":"Duclercq, Jerome","last_name":"Duclercq","first_name":"Jerome"},{"full_name":"Dokládal, Ladislav","last_name":"Dokládal","first_name":"Ladislav"},{"full_name":"Montesinos López, Juan C","first_name":"Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","orcid":"0000-0003-4675-6893","last_name":"Gallemi"},{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana"},{"full_name":"Rauter, Thomas","id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","last_name":"Rauter","first_name":"Thomas"},{"first_name":"Irene","last_name":"Stenzel","full_name":"Stenzel, Irene"},{"full_name":"Persiau, Geert","first_name":"Geert","last_name":"Persiau"},{"full_name":"Benade, Freia","last_name":"Benade","first_name":"Freia"},{"last_name":"Bhalearo","first_name":"Rishikesh","full_name":"Bhalearo, Rishikesh"},{"first_name":"Eva","last_name":"Sýkorová","full_name":"Sýkorová, Eva"},{"first_name":"András","last_name":"Gorzsás","full_name":"Gorzsás, András"},{"full_name":"Sechet, Julien","last_name":"Sechet","first_name":"Julien"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"full_name":"Ludwig-Müller, Jutta","last_name":"Ludwig-Müller","first_name":"Jutta"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"external_id":{"isi":["000531425900012"],"pmid":["32358503"]},"project":[{"call_identifier":"FWF","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"volume":11,"publication_identifier":{"eissn":["20411723"]},"isi":1,"day":"01","department":[{"_id":"EvBe"}],"quality_controlled":"1","oa":1,"file":[{"access_level":"open_access","file_name":"2020_NatureComm_Hurny.pdf","success":1,"date_created":"2020-10-06T07:47:53Z","checksum":"2cba327c9e9416d75cb96be54b0fb441","content_type":"application/pdf","file_size":4743576,"date_updated":"2020-10-06T07:47:53Z","creator":"dernst","file_id":"8614","relation":"main_file"}],"publisher":"Springer Nature","status":"public","date_created":"2020-05-10T22:00:48Z"},{"project":[{"grant_number":"P31312","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory"}],"volume":"2020-January","publication_identifier":{"isbn":["9781611975994"]},"author":[{"id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Filakovský","full_name":"Filakovský, Marek"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"},{"full_name":"Zhechev, Stephan Y","last_name":"Zhechev","first_name":"Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"We consider the following decision problem EMBEDk→d in computational topology (where k ≤ d are fixed positive integers): Given a finite simplicial complex K of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd?\r\nThe special case EMBED1→2 is graph planarity, which is decidable in linear time, as shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are known to be decidable (as well as NP-hard), and recent results of Čadek et al. in computational homotopy theory, in combination with the classical Haefliger–Weber theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial time for any fixed pair (k, d) of dimensions in the so-called metastable range .\r\nHere, by contrast, we prove that EMBEDk→d is algorithmically undecidable for almost all pairs of dimensions outside the metastable range, namely for . This almost completely resolves the decidability vs. undecidability of EMBEDk→d in higher dimensions and establishes a sharp dichotomy between polynomial-time solvability and undecidability.\r\nOur result complements (and in a wide range of dimensions strengthens) earlier results of Matoušek, Tancer, and the second author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard for all remaining pairs (k, d) outside the metastable range and satisfying d ≥ 4."}],"_id":"7806","status":"public","date_created":"2020-05-10T22:00:48Z","publisher":"SIAM","page":"767-785","quality_controlled":"1","oa":1,"day":"01","department":[{"_id":"UlWa"}],"oa_version":"Published Version","doi":"10.1137/1.9781611975994.47","conference":{"end_date":"2020-01-08","name":"SODA: Symposium on Discrete Algorithms","start_date":"2020-01-05","location":"Salt Lake City, UT, United States"},"month":"01","date_published":"2020-01-01T00:00:00Z","scopus_import":1,"citation":{"ieee":"M. Filakovský, U. Wagner, and S. Y. Zhechev, “Embeddability of simplicial complexes is undecidable,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 767–785.","mla":"Filakovský, Marek, et al. “Embeddability of Simplicial Complexes Is Undecidable.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2020–January, SIAM, 2020, pp. 767–85, doi:10.1137/1.9781611975994.47.","ama":"Filakovský M, Wagner U, Zhechev SY. Embeddability of simplicial complexes is undecidable. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2020-January. SIAM; 2020:767-785. doi:10.1137/1.9781611975994.47","ista":"Filakovský M, Wagner U, Zhechev SY. 2020. Embeddability of simplicial complexes is undecidable. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 767–785.","chicago":"Filakovský, Marek, Uli Wagner, and Stephan Y Zhechev. “Embeddability of Simplicial Complexes Is Undecidable.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2020–January:767–85. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.47.","apa":"Filakovský, M., Wagner, U., & Zhechev, S. Y. (2020). Embeddability of simplicial complexes is undecidable. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2020–January, pp. 767–785). Salt Lake City, UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.47","short":"M. Filakovský, U. Wagner, S.Y. Zhechev, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 767–785."},"date_updated":"2021-01-12T08:15:38Z","type":"conference","language":[{"iso":"eng"}],"year":"2020","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611975994.47"}],"title":"Embeddability of simplicial complexes is undecidable"},{"external_id":{"arxiv":["2003.13557"]},"author":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emo","last_name":"Welzl","full_name":"Welzl, Emo"}],"volume":"2020-January","publication_identifier":{"isbn":["9781611975994"]},"_id":"7807","abstract":[{"lang":"eng","text":"In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity.\r\nFor sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra).\r\nA corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"2823-2841","publisher":"SIAM","status":"public","date_created":"2020-05-10T22:00:48Z","department":[{"_id":"UlWa"}],"day":"01","arxiv":1,"oa":1,"quality_controlled":"1","related_material":{"record":[{"id":"12129","relation":"later_version","status":"public"}]},"conference":{"end_date":"2020-01-08","start_date":"2020-01-05","name":"SODA: Symposium on Discrete Algorithms","location":"Salt Lake City, UT, United States"},"doi":"10.1137/1.9781611975994.172","oa_version":"Submitted Version","date_updated":"2023-08-04T08:51:07Z","citation":{"short":"U. Wagner, E. Welzl, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 2823–2841.","apa":"Wagner, U., & Welzl, E. (2020). Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2020–January, pp. 2823–2841). Salt Lake City, UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.172","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2020–January:2823–41. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.172.","ista":"Wagner U, Welzl E. 2020. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 2823–2841.","ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2020-January. SIAM; 2020:2823-2841. doi:10.1137/1.9781611975994.172","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2020–January, SIAM, 2020, pp. 2823–41, doi:10.1137/1.9781611975994.172.","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane (Part I: Edge flips),” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 2823–2841."},"type":"conference","scopus_import":1,"month":"01","date_published":"2020-01-01T00:00:00Z","article_processing_charge":"No","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"year":"2020","title":"Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611975994.172"}]}]