[{"month":"05","publisher":"American Chemical Society","main_file_link":[{"open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s002","related_material":{"record":[{"id":"8040","status":"public","relation":"used_in_publication"}]},"date_created":"2021-04-14T12:05:20Z","day":"20","year":"2020","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"9326","department":[{"_id":"LeSa"}],"title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","author":[{"last_name":"Gupta","full_name":"Gupta, Chitrak","first_name":"Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"last_name":"Chan","full_name":"Chan, Chun","first_name":"Chun"},{"first_name":"Francois","last_name":"Dehez","full_name":"Dehez, Francois"},{"first_name":"Mrinal","full_name":"Shekhar, Mrinal","last_name":"Shekhar"},{"full_name":"Gunner, M. R.","last_name":"Gunner","first_name":"M. R."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"full_name":"Singharoy, Abhishek","last_name":"Singharoy","first_name":"Abhishek"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T07:49:37Z","citation":{"mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002."}},{"_id":"8042","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-22T07:47:04Z","department":[{"_id":"RoSe"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N."}],"intvolume":" 22","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04819"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["14359855"]},"volume":22,"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403, 2020.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966","mla":"Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. European Mathematical Society, 2020. https://doi.org/10.4171/JEMS/966."},"title":"The excitation spectrum of Bose gases interacting through singular potentials","article_processing_charge":"No","external_id":{"isi":["000548174700006"],"arxiv":["1704.04819"]},"author":[{"last_name":"Boccato","full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara"},{"first_name":"Christian","full_name":"Brennecke, Christian","last_name":"Brennecke"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"}],"oa":1,"publisher":"European Mathematical Society","quality_controlled":"1","publication":"Journal of the European Mathematical Society","day":"01","year":"2020","isi":1,"date_created":"2020-06-29T07:59:35Z","date_published":"2020-07-01T00:00:00Z","doi":"10.4171/JEMS/966","page":"2331-2403"},{"status":"public","type":"research_data_reference","_id":"9713","department":[{"_id":"LeSa"}],"title":"Supporting information","author":[{"last_name":"Gupta","full_name":"Gupta, Chitrak","first_name":"Chitrak"},{"first_name":"Umesh","full_name":"Khaniya, Umesh","last_name":"Khaniya"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"last_name":"Dehez","full_name":"Dehez, Francois","first_name":"Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"first_name":"M.R.","last_name":"Gunner","full_name":"Gunner, M.R."},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-22T07:49:38Z","citation":{"ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Supporting information.” American Chemical Society , 2020.","mla":"Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001."},"month":"05","publisher":"American Chemical Society ","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Additional analyses of the trajectories"}],"doi":"10.1021/jacs.9b13450.s001","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"status":"public","id":"8040","relation":"used_in_publication"}]},"date_created":"2021-07-23T12:02:39Z","day":"20","year":"2020"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-22T07:49:38Z","citation":{"mla":"Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ama":"Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002","ieee":"C. Gupta et al., “Movies.” American Chemical Society, 2020.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002."},"title":"Movies","department":[{"_id":"LeSa"}],"article_processing_charge":"No","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"last_name":"Chan","full_name":"Chan, Chun Kit","first_name":"Chun Kit"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"first_name":"Mrinal","last_name":"Shekhar","full_name":"Shekhar, Mrinal"},{"first_name":"M.R.","full_name":"Gunner, M.R.","last_name":"Gunner"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"first_name":"Abhishek","last_name":"Singharoy","full_name":"Singharoy, Abhishek"}],"_id":"9878","status":"public","type":"research_data_reference","day":"20","year":"2020","date_created":"2021-08-11T09:18:54Z","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8040"}]},"doi":"10.1021/jacs.9b13450.s002","oa_version":"Published Version","month":"05","publisher":"American Chemical Society"},{"citation":{"chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.","ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954.","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32601464"],"isi":["000544152500001"]},"article_processing_charge":"No","author":[{"last_name":"Hippe","full_name":"Hippe, Andreas","first_name":"Andreas"},{"first_name":"Stephan Alexander","full_name":"Braun, Stephan Alexander","last_name":"Braun"},{"full_name":"Oláh, Péter","last_name":"Oláh","first_name":"Péter"},{"first_name":"Peter Arne","full_name":"Gerber, Peter Arne","last_name":"Gerber"},{"first_name":"Anne","full_name":"Schorr, Anne","last_name":"Schorr"},{"first_name":"Stephan","full_name":"Seeliger, Stephan","last_name":"Seeliger"},{"first_name":"Stephanie","full_name":"Holtz, Stephanie","last_name":"Holtz"},{"first_name":"Katharina","last_name":"Jannasch","full_name":"Jannasch, Katharina"},{"last_name":"Pivarcsi","full_name":"Pivarcsi, Andor","first_name":"Andor"},{"first_name":"Bettina","full_name":"Buhren, Bettina","last_name":"Buhren"},{"first_name":"Holger","last_name":"Schrumpf","full_name":"Schrumpf, Holger"},{"full_name":"Kislat, Andreas","last_name":"Kislat","first_name":"Andreas"},{"last_name":"Bünemann","full_name":"Bünemann, Erich","first_name":"Erich"},{"first_name":"Martin","full_name":"Steinhoff, Martin","last_name":"Steinhoff"},{"last_name":"Fischer","full_name":"Fischer, Jens","first_name":"Jens"},{"full_name":"Lira, Sérgio A.","last_name":"Lira","first_name":"Sérgio A."},{"first_name":"Petra","last_name":"Boukamp","full_name":"Boukamp, Petra"},{"first_name":"Peter","last_name":"Hevezi","full_name":"Hevezi, Peter"},{"first_name":"Nikolas Hendrik","full_name":"Stoecklein, Nikolas Hendrik","last_name":"Stoecklein"},{"last_name":"Hoffmann","full_name":"Hoffmann, Thomas","first_name":"Thomas"},{"last_name":"Alves","full_name":"Alves, Frauke","first_name":"Frauke"},{"last_name":"Sleeman","full_name":"Sleeman, Jonathan","first_name":"Jonathan"},{"full_name":"Bauer, Thomas","last_name":"Bauer","first_name":"Thomas"},{"last_name":"Klufa","full_name":"Klufa, Jörg","first_name":"Jörg"},{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"},{"first_name":"Albert","full_name":"Zlotnik, Albert","last_name":"Zlotnik"},{"full_name":"Müller-Homey, Anja","last_name":"Müller-Homey","first_name":"Anja"},{"first_name":"Bernhard","full_name":"Homey, Bernhard","last_name":"Homey"}],"title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","year":"2020","has_accepted_license":"1","isi":1,"publication":"British Journal of Cancer","day":"15","page":"942-954","date_created":"2020-07-05T22:00:46Z","date_published":"2020-09-15T00:00:00Z","doi":"10.1038/s41416-020-0943-2","acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-08-22T07:51:12Z","ddc":["610"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-12-02T12:35:12Z","_id":"8093","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0007-0920"],"eissn":["1532-1827"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","file_id":"10398","success":1,"date_updated":"2021-12-02T12:35:12Z","file_size":3620691,"creator":"cchlebak","date_created":"2021-12-02T12:35:12Z","file_name":"2020_BrJournalCancer_Hippe.pdf"}],"volume":123,"related_material":{"record":[{"relation":"later_version","status":"deleted","id":"10170"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}]},"abstract":[{"lang":"eng","text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 123","month":"09"},{"abstract":[{"text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 181","publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8812","checksum":"5cbeef52caf18d0d952f17fed7b5545a","success":1,"date_updated":"2020-11-25T15:05:04Z","file_size":404778,"creator":"dernst","date_created":"2020-11-25T15:05:04Z","file_name":"2020_JourStatPhysics_Seiringer.pdf"}],"language":[{"iso":"eng"}],"volume":181,"ec_funded":1,"_id":"8091","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-22T07:51:47Z","ddc":["530"],"file_date_updated":"2020-11-25T15:05:04Z","department":[{"_id":"RoSe"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","publisher":"Springer","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Journal of Statistical Physics","page":"448-464","date_published":"2020-10-01T00:00:00Z","doi":"10.1007/s10955-020-02586-0","date_created":"2020-07-05T22:00:46Z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464.","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yngvason","full_name":"Yngvason, Jakob","first_name":"Jakob"}],"external_id":{"arxiv":["2001.07144"],"isi":["000543030000002"]},"article_processing_charge":"Yes (via OA deal)","title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions"},{"acknowledgement":"The authors are grateful to the two anonymous referees for their insightful comments and suggestions which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013) (Grant agreement No. 616160).","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Applied Numerical Mathematics","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-07-02T09:02:33Z","date_published":"2020-11-01T00:00:00Z","doi":"10.1016/j.apnum.2020.06.009","page":"315-337","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 2020;157:315-337. doi:10.1016/j.apnum.2020.06.009","apa":"Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009","short":"Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.","ieee":"Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence,” Applied Numerical Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009.","ista":"Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 157, 315–337.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009."},"title":"Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence","article_processing_charge":"No","external_id":{"isi":["000564648400018"]},"author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139"},{"last_name":"Iyiola","full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S."}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods."}],"intvolume":" 157","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:09Z","file_size":2874203,"creator":"dernst","date_created":"2020-07-02T09:08:59Z","file_name":"2020_AppliedNumericalMath_Shehu.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8078","checksum":"87d81324a62c82baa925c009dfcb0200"}],"publication_status":"published","publication_identifier":{"issn":["0168-9274"]},"ec_funded":1,"volume":157,"_id":"8077","status":"public","article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-08-22T07:50:43Z","department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:48:09Z"},{"status":"public","type":"journal_article","article_type":"original","_id":"8039","department":[{"_id":"MaIb"}],"date_updated":"2023-08-22T07:50:08Z","month":"06","intvolume":" 12","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"In the present work, we report a solution-based strategy to produce crystallographically textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric performance in the direction normal to the substrate. Our strategy is based on the formulation of a molecular precursor that can be continuously decomposed to produce a SnSe powder or printed into predefined patterns. The precursor formulation and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates. The printed layer and the bulk material obtained after hot press displays a clear preferential orientation of the crystallographic domains, resulting in an ultralow thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate. Such textured nanomaterials present highly anisotropic properties with the best thermoelectric performance in plane, i.e., in the directions parallel to the substrate, which coincide with the crystallographic bc plane of SnSe. This is an unfortunate characteristic because thermoelectric devices are designed to create/harvest temperature gradients in the direction normal to the substrate. We further demonstrate that this limitation can be overcome with the introduction of small amounts of tellurium in the precursor. The presence of tellurium allows one to reduce the band gap and increase both the charge carrier concentration and the mobility, especially the cross plane, with a minimal decrease of the Seebeck coefficient. These effects translate into record out of plane ZT values at 800 K.","lang":"eng"}],"volume":12,"issue":"24","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19448252"]},"publication_status":"published","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"title":"Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices","author":[{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"last_name":"Xing","full_name":"Xing, Congcong","first_name":"Congcong"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"first_name":"Mengyao","full_name":"Li, Mengyao","last_name":"Li"},{"first_name":"Mercè","last_name":"Pacios","full_name":"Pacios, Mercè"},{"first_name":"Xiaoting","last_name":"Yu","full_name":"Yu, Xiaoting"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"article_processing_charge":"No","external_id":{"isi":["000542925300032"],"pmid":["32437128"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zhang Y, Liu Y, Xing C, Zhang T, Li M, Pacios M, Yu X, Arbiol J, Llorca J, Cadavid D, Ibáñez M, Cabot A. 2020. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 12(24), 27104–27111.","chicago":"Zhang, Yu, Yu Liu, Congcong Xing, Ting Zhang, Mengyao Li, Mercè Pacios, Xiaoting Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces. American Chemical Society, 2020. https://doi.org/10.1021/acsami.0c04331.","short":"Y. Zhang, Y. Liu, C. Xing, T. Zhang, M. Li, M. Pacios, X. Yu, J. Arbiol, J. Llorca, D. Cadavid, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 12 (2020) 27104–27111.","ieee":"Y. Zhang et al., “Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices,” ACS Applied Materials and Interfaces, vol. 12, no. 24. American Chemical Society, pp. 27104–27111, 2020.","apa":"Zhang, Y., Liu, Y., Xing, C., Zhang, T., Li, M., Pacios, M., … Cabot, A. (2020). Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.0c04331","ama":"Zhang Y, Liu Y, Xing C, et al. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 2020;12(24):27104-27111. doi:10.1021/acsami.0c04331","mla":"Zhang, Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces, vol. 12, no. 24, American Chemical Society, 2020, pp. 27104–11, doi:10.1021/acsami.0c04331."},"quality_controlled":"1","publisher":"American Chemical Society","date_published":"2020-06-17T00:00:00Z","doi":"10.1021/acsami.0c04331","date_created":"2020-06-29T07:59:35Z","page":"27104-27111","day":"17","publication":"ACS Applied Materials and Interfaces","isi":1,"year":"2020"},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"Genome Medicine","day":"08","date_created":"2020-07-19T22:00:58Z","doi":"10.1186/s13073-020-00754-1","date_published":"2020-07-08T00:00:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).","ieee":"R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32641083"],"isi":["000551778400001"]},"article_processing_charge":"No","author":[{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel","first_name":"Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"last_name":"Mccartney","full_name":"Mccartney, Daniel L.","first_name":"Daniel L."},{"first_name":"Sarah E.","full_name":"Harris, Sarah E.","last_name":"Harris"},{"last_name":"Stevenson","full_name":"Stevenson, Anna J.","first_name":"Anna J."},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"full_name":"Zhang, Qian","last_name":"Zhang","first_name":"Qian"},{"last_name":"Liewald","full_name":"Liewald, David C.","first_name":"David C."},{"last_name":"Ritchie","full_name":"Ritchie, Craig W.","first_name":"Craig W."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"first_name":"Elliot M.","full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob"},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"first_name":"Allan F.","full_name":"Mcrae, Allan F.","last_name":"Mcrae"},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."}],"title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","article_number":"60","publication_status":"published","publication_identifier":{"eissn":["1756994X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8145","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_GenomeMedicine_Hillary.pdf","date_created":"2020-07-22T06:27:38Z","file_size":1136983,"date_updated":"2020-07-22T06:27:38Z","creator":"dernst"}],"related_material":{"record":[{"status":"public","id":"9706","relation":"research_data"}]},"volume":12,"issue":"1","abstract":[{"lang":"eng","text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 12","month":"07","date_updated":"2023-08-22T07:55:37Z","ddc":["570"],"department":[{"_id":"MaRo"}],"file_date_updated":"2020-07-22T06:27:38Z","_id":"8133","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"date_created":"2020-07-16T12:26:04Z","doi":"10.7554/eLife.56261","date_published":"2020-09-17T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"17","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","article_processing_charge":"No","external_id":{"isi":["000584989400001"],"pmid":["32940606"]},"author":[{"first_name":"Pedro J.","full_name":"Gonçalves, Pedro J.","orcid":"0000-0002-6987-4836","last_name":"Gonçalves"},{"first_name":"Jan-Matthis","last_name":"Lueckmann","orcid":"0000-0003-4320-4663","full_name":"Lueckmann, Jan-Matthis"},{"full_name":"Deistler, Michael","orcid":"0000-0002-3573-0404","last_name":"Deistler","first_name":"Michael"},{"first_name":"Marcel","last_name":"Nonnenmacher","full_name":"Nonnenmacher, Marcel","orcid":"0000-0001-6044-6627"},{"last_name":"Öcal","full_name":"Öcal, Kaan","orcid":"0000-0002-8528-6858","first_name":"Kaan"},{"full_name":"Bassetto, Giacomo","last_name":"Bassetto","first_name":"Giacomo"},{"id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","first_name":"Chaitanya","last_name":"Chintaluri","orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya"},{"first_name":"William F.","last_name":"Podlaski","orcid":"0000-0001-6619-7502","full_name":"Podlaski, William F."},{"full_name":"Haddad, Sara A.","orcid":"0000-0003-0807-0823","last_name":"Haddad","first_name":"Sara A."},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"},{"full_name":"Greenberg, David S.","last_name":"Greenberg","first_name":"David S."},{"first_name":"Jakob H.","last_name":"Macke","full_name":"Macke, Jakob H.","orcid":"0000-0001-5154-8912"}],"title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","citation":{"mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"article_number":"e56261","ec_funded":1,"volume":9,"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","file_id":"8709","success":1,"date_updated":"2020-10-27T11:37:32Z","file_size":17355867,"creator":"cziletti","date_created":"2020-10-27T11:37:32Z","file_name":"2020_eLife_Gonçalves.pdf"}],"scopus_import":"1","intvolume":" 9","month":"09","abstract":[{"text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"TiVo"}],"file_date_updated":"2020-10-27T11:37:32Z","date_updated":"2023-08-22T07:54:52Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8127"},{"quality_controlled":"1","publisher":"Society for Neuroscience","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"09","publication":"The Journal of Neuroscience","page":"9634-9649","date_published":"2020-12-09T00:00:00Z","doi":"10.1523/JNEUROSCI.0276-20.2020","date_created":"2020-07-16T12:25:04Z","citation":{"mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020.","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.","ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Agnes","orcid":"0000-0001-7184-7311","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"last_name":"Luppi","full_name":"Luppi, Andrea I.","first_name":"Andrea I."},{"last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"external_id":{"pmid":["33168622"],"isi":["000606706400009"]},"article_processing_charge":"No","title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","abstract":[{"lang":"eng","text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"12","intvolume":" 40","publication_identifier":{"eissn":["1529-2401"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"7977e4dd6b89357d1a5cc88babac56da","file_id":"8977","creator":"dernst","file_size":2750920,"date_updated":"2020-12-28T08:31:47Z","file_name":"2020_JourNeuroscience_Agnes.pdf","date_created":"2020-12-28T08:31:47Z"}],"language":[{"iso":"eng"}],"volume":40,"issue":"50","_id":"8126","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-22T07:54:26Z","ddc":["570"],"department":[{"_id":"TiVo"}],"file_date_updated":"2020-12-28T08:31:47Z"},{"article_number":"eabc3979","title":"The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity","external_id":{"pmid":["32646852"],"isi":["000546994600004"]},"article_processing_charge":"No","author":[{"first_name":"Elisabeth","full_name":"Salzer, Elisabeth","last_name":"Salzer"},{"first_name":"Samaneh","full_name":"Zoghi, Samaneh","last_name":"Zoghi"},{"full_name":"Kiss, Máté G.","last_name":"Kiss","first_name":"Máté G."},{"last_name":"Kage","full_name":"Kage, Frieda","first_name":"Frieda"},{"first_name":"Christina","last_name":"Rashkova","full_name":"Rashkova, Christina"},{"last_name":"Stahnke","full_name":"Stahnke, Stephanie","first_name":"Stephanie"},{"first_name":"Matthias","full_name":"Haimel, Matthias","last_name":"Haimel"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"first_name":"Michael","last_name":"Caldera","full_name":"Caldera, Michael"},{"last_name":"Ardy","full_name":"Ardy, Rico Chandra","first_name":"Rico Chandra"},{"first_name":"Birgit","full_name":"Hoeger, Birgit","last_name":"Hoeger"},{"last_name":"Block","full_name":"Block, Jana","first_name":"Jana"},{"first_name":"David","last_name":"Medgyesi","full_name":"Medgyesi, David"},{"first_name":"Celine","full_name":"Sin, Celine","last_name":"Sin"},{"first_name":"Sepideh","last_name":"Shahkarami","full_name":"Shahkarami, Sepideh"},{"full_name":"Kain, Renate","last_name":"Kain","first_name":"Renate"},{"full_name":"Ziaee, Vahid","last_name":"Ziaee","first_name":"Vahid"},{"first_name":"Peter","full_name":"Hammerl, Peter","last_name":"Hammerl"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"full_name":"Dupré, Loïc","last_name":"Dupré","first_name":"Loïc"},{"last_name":"Huppa","full_name":"Huppa, Johannes B.","first_name":"Johannes B."},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Alexis","full_name":"Lomakin, Alexis","last_name":"Lomakin"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"first_name":"Christoph J.","full_name":"Binder, Christoph J.","last_name":"Binder"},{"full_name":"Stradal, Theresia E.B.","last_name":"Stradal","first_name":"Theresia E.B."},{"full_name":"Rezaei, Nima","last_name":"Rezaei","first_name":"Nima"},{"first_name":"Kaan","full_name":"Boztug, Kaan","last_name":"Boztug"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology. AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.","ista":"Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 5(49), eabc3979.","mla":"Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979, AAAS, 2020, doi:10.1126/sciimmunol.abc3979.","ieee":"E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.","short":"E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel, R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S. Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B. Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei, K. Boztug, Science Immunology 5 (2020).","apa":"Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., … Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979","ama":"Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 2020;5(49). doi:10.1126/sciimmunol.abc3979"},"quality_controlled":"1","publisher":"AAAS","date_created":"2020-07-19T22:00:58Z","doi":"10.1126/sciimmunol.abc3979","date_published":"2020-07-10T00:00:00Z","publication":"Science Immunology","day":"10","year":"2020","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"8132","department":[{"_id":"MiSi"}],"date_updated":"2023-08-22T07:56:04Z","intvolume":" 5","month":"07","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity."}],"volume":5,"issue":"49","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["24709468"]}},{"other_data_license":"CC0 + CC BY (4.0)","month":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19)."}],"date_created":"2021-07-23T08:59:15Z","date_published":"2020-07-09T00:00:00Z","doi":"10.6084/m9.figshare.12629697.v1","related_material":{"record":[{"id":"8133","status":"public","relation":"used_in_publication"}]},"day":"09","year":"2020","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"9706","department":[{"_id":"MaRo"}],"title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","article_processing_charge":"No","author":[{"first_name":"Robert F.","full_name":"Hillary, Robert F.","last_name":"Hillary"},{"last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel","first_name":"Daniel"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"first_name":"Daniel L.","full_name":"McCartney, Daniel L.","last_name":"McCartney"},{"first_name":"Sarah E.","last_name":"Harris","full_name":"Harris, Sarah E."},{"full_name":"Stevenson, Anna J.","last_name":"Stevenson","first_name":"Anna J."},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"first_name":"Qian","full_name":"Zhang, Qian","last_name":"Zhang"},{"last_name":"Liewald","full_name":"Liewald, David C.","first_name":"David C."},{"first_name":"Craig W.","full_name":"Ritchie, Craig W.","last_name":"Ritchie"},{"last_name":"Evans","full_name":"Evans, Kathryn L.","first_name":"Kathryn L."},{"last_name":"Tucker-Drob","full_name":"Tucker-Drob, Elliot M.","first_name":"Elliot M."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"first_name":"Allan F. ","full_name":"McRae, Allan F. ","last_name":"McRae"},{"first_name":"Peter M.","full_name":"Visscher, Peter M.","last_name":"Visscher"},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Marioni, Riccardo E. ","last_name":"Marioni","first_name":"Riccardo E. "}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020."},"date_updated":"2023-08-22T07:55:36Z"},{"article_number":"061901","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950.","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2002.08281"],"isi":["000544595100001"]},"article_processing_charge":"No","author":[{"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","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","year":"2020","isi":1,"publication":"Journal of Mathematical Physics","day":"22","date_created":"2020-07-19T22:00:59Z","doi":"10.1063/5.0005950","date_published":"2020-06-22T00:00:00Z","_id":"8134","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T08:12:40Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"scopus_import":"1","intvolume":" 61","month":"06","publication_status":"published","publication_identifier":{"issn":["00222488"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6","volume":61},{"year":"2020","isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","day":"12","date_created":"2020-07-13T03:41:39Z","doi":"10.1098/rstb.2019.0530","date_published":"2020-07-12T00:00:00Z","quality_controlled":"1","publisher":"The Royal Society","citation":{"ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530","apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["32654647"],"isi":["000552662100002"]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"On the completion of speciation","article_number":"20190530","publication_status":"published","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"language":[{"iso":"eng"}],"issue":"1806","volume":375,"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 375","month":"07","date_updated":"2023-08-22T07:53:52Z","department":[{"_id":"NiBa"}],"_id":"8112","article_type":"letter_note","type":"journal_article","status":"public"},{"status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"8162","file_date_updated":"2020-12-02T09:26:46Z","department":[{"_id":"SiHi"}],"ddc":["570"],"date_updated":"2023-08-22T08:20:11Z","month":"09","intvolume":" 107","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"issue":"6","volume":107,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/","description":"News on IST Website"}]},"ec_funded":1,"file":[{"creator":"dernst","file_size":8911830,"date_updated":"2020-12-02T09:26:46Z","file_name":"2020_Neuron_Laukoter.pdf","date_created":"2020-12-02T09:26:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"7becdc16a6317304304631087ae7dd7f","file_id":"8828"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"title":"Cell-type specificity of genomic imprinting in cerebral cortex","author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Beattie","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","last_name":"Hansen"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Penz","full_name":"Penz, Thomas"},{"orcid":"0000-0001-6091-3088","full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000579698700006"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","ieee":"S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","date_published":"2020-09-23T00:00:00Z","doi":"10.1016/j.neuron.2020.06.031","date_created":"2020-07-23T16:03:12Z","page":"1160-1179.e9","day":"23","publication":"Neuron","has_accepted_license":"1","isi":1,"year":"2020"},{"language":[{"iso":"eng"}],"file":[{"file_size":1759490,"date_updated":"2020-07-22T08:32:55Z","creator":"dernst","file_name":"2020_NatureComm_Zhang.pdf","date_created":"2020-07-22T08:32:55Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8148"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"volume":11,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"issue":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.","lang":"eng"}],"intvolume":" 11","month":"07","scopus_import":"1","ddc":["580"],"date_updated":"2023-08-22T08:13:44Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-22T08:32:55Z","_id":"8138","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Nature Communications","day":"14","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-07-21T08:58:07Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1038/s41467-020-17252-y","page":"3508","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y","ieee":"J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508."},"title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","external_id":{"pmid":["32665554"],"isi":["000550062200004"]},"article_processing_charge":"No","author":[{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"},{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"last_name":"Balla","full_name":"Balla, J","first_name":"J"},{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"full_name":"Kalousek, P","last_name":"Kalousek","first_name":"P"},{"first_name":"Z","full_name":"Medveďová, Z","last_name":"Medveďová"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"last_name":"Wang","full_name":"Wang, Y","first_name":"Y"},{"first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","full_name":"Prat, Tomas"},{"first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","full_name":"Vasileva, Mina K"},{"last_name":"Reinöhl","full_name":"Reinöhl, V","first_name":"V"},{"last_name":"Procházka","full_name":"Procházka, S","first_name":"S"},{"first_name":"R","last_name":"Halouzka","full_name":"Halouzka, R"},{"first_name":"P","last_name":"Tarkowski","full_name":"Tarkowski, P"},{"last_name":"Luschnig","full_name":"Luschnig, C","first_name":"C"},{"full_name":"Brewer, PB","last_name":"Brewer","first_name":"PB"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}]},{"publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","day":"12","year":"2020","isi":1,"date_created":"2020-07-26T22:01:01Z","doi":"10.1098/rstb.2019.0528","date_published":"2020-07-12T00:00:00Z","oa":1,"publisher":"The Royal Society","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528."},"title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","external_id":{"pmid":["32654637"],"isi":["000552662100001"]},"article_processing_charge":"No","author":[{"first_name":"Jonna","full_name":"Kulmuni, Jonna","last_name":"Kulmuni"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Kay","full_name":"Lucek, Kay","last_name":"Lucek"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"article_number":"20190528","project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"ec_funded":1,"volume":375,"issue":"1806","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"intvolume":" 375","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"scopus_import":"1","date_updated":"2023-08-22T08:21:31Z","department":[{"_id":"NiBa"}],"_id":"8168","status":"public","type":"journal_article","article_type":"original"},{"_id":"8167","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-22T08:22:13Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.","lang":"eng"}],"month":"07","intvolume":" 375","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0545"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1471-2970"]},"publication_status":"published","issue":"1806","volume":375,"article_number":"20190545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545."},"title":"The evolution of strong reproductive isolation between sympatric intertidal snails","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B."},{"last_name":"Eyres","full_name":"Eyres, Isobel","first_name":"Isobel"},{"first_name":"Thomas","last_name":"Broquet","full_name":"Broquet, Thomas"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"article_processing_charge":"No","external_id":{"pmid":["32654639"],"isi":["000552662100014"]},"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","quality_controlled":"1","publisher":"The Royal Society","oa":1,"day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","isi":1,"year":"2020","date_published":"2020-07-12T00:00:00Z","doi":"10.1098/rstb.2019.0545","date_created":"2020-07-26T22:01:01Z"},{"date_created":"2020-07-26T22:01:02Z","date_published":"2020-07-03T00:00:00Z","doi":"10.1103/PhysRevLett.125.013001","year":"2020","isi":1,"publication":"Physical Review Letters","day":"03","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"article_processing_charge":"No","author":[{"last_name":"Chatterley","full_name":"Chatterley, Adam S.","first_name":"Adam S."},{"last_name":"Christiansen","full_name":"Christiansen, Lars","first_name":"Lars"},{"full_name":"Schouder, Constant A.","last_name":"Schouder","first_name":"Constant A."},{"last_name":"Jørgensen","full_name":"Jørgensen, Anders V.","first_name":"Anders V."},{"first_name":"Benjamin","full_name":"Shepperson, Benjamin","last_name":"Shepperson"},{"first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert E.","full_name":"Zillich, Robert E.","last_name":"Zillich"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt","first_name":"Henrik"}],"title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","citation":{"mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001.","ieee":"A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020.","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"013001","ec_funded":1,"volume":125,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}],"scopus_import":"1","intvolume":" 125","month":"07","abstract":[{"lang":"eng","text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes."}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2023-08-22T08:22:43Z","type":"journal_article","article_type":"original","status":"public","_id":"8170"},{"_id":"8194","status":"public","conference":{"name":"IJCAR: International Joint Conference on Automated Reasoning","start_date":"2020-07-01","location":"Paris, France","end_date":"2020-07-04"},"type":"conference","date_updated":"2023-08-22T08:27:25Z","department":[{"_id":"ToHe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"intvolume":" 12166","month":"06","main_file_link":[{"url":"https://doi.org/10.1007/978-3-030-51074-9_2","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030510732"],"eissn":["16113349"],"issn":["03029743"]},"volume":12166,"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31."},"title":"An SMT theory of fixed-point arithmetic","external_id":{"isi":["000884318000002"]},"article_processing_charge":"No","author":[{"last_name":"Baranowski","full_name":"Baranowski, Marek","first_name":"Marek"},{"first_name":"Shaobo","full_name":"He, Shaobo","last_name":"He"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"first_name":"Thanh Son","full_name":"Nguyen, Thanh Son","last_name":"Nguyen"},{"first_name":"Zvonimir","full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Automated Reasoning","day":"24","year":"2020","isi":1,"date_created":"2020-08-02T22:00:59Z","doi":"10.1007/978-3-030-51074-9_2","date_published":"2020-06-24T00:00:00Z","page":"13-31"},{"article_number":"20190544","article_processing_charge":"No","external_id":{"pmid":["32654641"],"isi":["000552662100013"]},"author":[{"last_name":"Shang","full_name":"Shang, Huiying","first_name":"Huiying"},{"first_name":"Jaqueline","full_name":"Hess, Jaqueline","last_name":"Hess"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pär K.","last_name":"Ingvarsson","full_name":"Ingvarsson, Pär K."},{"first_name":"Jianquan","last_name":"Liu","full_name":"Liu, Jianquan"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"}],"title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","citation":{"ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.","ieee":"H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"The Royal Society","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","date_created":"2020-07-26T22:01:02Z","doi":"10.1098/rstb.2019.0544","date_published":"2020-07-12T00:00:00Z","year":"2020","isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","day":"12","article_type":"original","type":"journal_article","status":"public","_id":"8169","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T08:23:24Z","scopus_import":"1","intvolume":" 375","month":"07","abstract":[{"lang":"eng","text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation."}],"pmid":1,"oa_version":"Published Version","issue":"1806","volume":375,"publication_status":"published","publication_identifier":{"eissn":["14712970"]},"language":[{"iso":"eng"}]},{"acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","publisher":"Elsevier","quality_controlled":"1","isi":1,"year":"2020","day":"01","publication":"Nano Energy","doi":"10.1016/j.nanoen.2020.105116","date_published":"2020-11-01T00:00:00Z","date_created":"2020-08-02T22:00:57Z","article_number":"105116","citation":{"mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020, doi:10.1016/j.nanoen.2020.105116.","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116","ieee":"X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116.","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Xiaoting","full_name":"Yu, Xiaoting","last_name":"Yu"},{"first_name":"Junfeng","last_name":"Liu","full_name":"Liu, Junfeng"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"full_name":"Luo, Zhishan","last_name":"Luo","first_name":"Zhishan"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"first_name":"Congcong","full_name":"Xing, Congcong","last_name":"Xing"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"last_name":"Nasiou","full_name":"Nasiou, Déspina","first_name":"Déspina"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"last_name":"Pan","full_name":"Pan, Kai","first_name":"Kai"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"last_name":"Xie","full_name":"Xie, Ying","first_name":"Ying"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"external_id":{"isi":["000581738300030"]},"article_processing_charge":"No","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","abstract":[{"text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"11","intvolume":" 77","publication_identifier":{"issn":["2211-2855"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":77,"issue":"11","_id":"8189","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T08:24:05Z","department":[{"_id":"MaIb"}]},{"has_accepted_license":"1","isi":1,"year":"2020","day":"21","publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"16969-16975","doi":"10.1073/pnas.1921205117","date_published":"2020-07-21T00:00:00Z","date_created":"2020-08-09T22:00:52Z","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"citation":{"ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi"},{"first_name":"Saskia I.J.","full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Jacco","last_name":"Van Rheenen","full_name":"Van Rheenen, Jacco"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"article_processing_charge":"No","title":"Stem cell lineage survival as a noisy competition for niche access","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"publication_identifier":{"eissn":["10916490"]},"publication_status":"published","file":[{"date_updated":"2020-08-10T06:50:28Z","file_size":1111604,"creator":"dernst","date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8223","success":1}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"issue":"29","volume":117,"ec_funded":1,"abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 117","date_updated":"2023-08-22T08:29:30Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-08-10T06:50:28Z","_id":"8220","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"abstract":[{"lang":"eng","text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"07","publication_status":"published","publication_identifier":{"issn":["2542-4653"]},"language":[{"iso":"eng"}],"file":[{"file_size":531137,"date_updated":"2020-08-06T08:56:06Z","creator":"dernst","file_name":"2020_SciPostPhys_Gulden.pdf","date_created":"2020-08-06T08:56:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8202"}],"ec_funded":1,"volume":9,"_id":"8199","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T08:28:24Z","ddc":["530"],"department":[{"_id":"MaSe"}],"file_date_updated":"2020-08-06T08:56:06Z","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","oa":1,"quality_controlled":"1","publisher":"SciPost Foundation","year":"2020","has_accepted_license":"1","isi":1,"publication":"SciPost Physics","day":"29","date_created":"2020-08-04T13:04:15Z","doi":"10.21468/scipostphys.9.1.015","date_published":"2020-07-29T00:00:00Z","article_number":"015","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020.","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000557362300008"]},"author":[{"first_name":"Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer","last_name":"Rudner"},{"last_name":"Lindner","full_name":"Lindner, Netanel","first_name":"Netanel"}],"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps"},{"date_updated":"2023-08-22T08:30:55Z","ddc":["570"],"file_date_updated":"2020-12-04T09:29:21Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"_id":"8261","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","file":[{"success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_id":"8920","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Neuron_Zhang.pdf","date_created":"2020-12-04T09:29:21Z","creator":"dernst","file_size":3011120,"date_updated":"2020-12-04T09:29:21Z"}],"language":[{"iso":"eng"}],"volume":107,"issue":"6","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"abstract":[{"text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"month":"09","intvolume":" 107","citation":{"chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.","apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"article_processing_charge":"No","external_id":{"isi":["000579698700009"],"pmid":["32763145"]},"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"23","publication":"Neuron","page":"1212-1225","doi":"10.1016/j.neuron.2020.07.006","date_published":"2020-09-23T00:00:00Z","date_created":"2020-08-14T09:36:05Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","quality_controlled":"1","publisher":"Elsevier","oa":1},{"author":[{"full_name":"Gurel, Nezihe Merve","last_name":"Gurel","first_name":"Nezihe Merve"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"full_name":"Smith, Tyler","last_name":"Smith","first_name":"Tyler"},{"first_name":"Thomas","full_name":"Lemmin, Thomas","last_name":"Lemmin"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Markus","full_name":"Puschel, Markus","last_name":"Puschel"},{"full_name":"Zhang, Ce","last_name":"Zhang","first_name":"Ce"}],"external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"article_processing_charge":"No","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","citation":{"ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","ieee":"N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"4268-4282","date_published":"2020-07-20T00:00:00Z","doi":"10.1109/TSP.2020.3010355","date_created":"2020-08-16T22:00:56Z","isi":1,"year":"2020","day":"20","publication":"IEEE Transactions on Signal Processing","quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","department":[{"_id":"DaAl"}],"date_updated":"2023-08-22T08:40:08Z","article_type":"original","type":"journal_article","status":"public","_id":"8268","volume":68,"publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.04907"}],"month":"07","intvolume":" 68","abstract":[{"text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.","lang":"eng"}],"oa_version":"Preprint"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","apa":"He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006","mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006."},"title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","external_id":{"pmid":["32688032"],"isi":["000566895400007"]},"article_processing_charge":"No","author":[{"first_name":"Peng","last_name":"He","full_name":"He, Peng"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xiao","full_name":"Xiao, Guanghui","first_name":"Guanghui"}],"publication":"Molecular Plant","day":"07","year":"2020","isi":1,"date_created":"2020-08-16T22:00:57Z","doi":"10.1016/j.molp.2020.07.006","date_published":"2020-09-07T00:00:00Z","page":"1238-1240","acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-08-22T08:40:35Z","department":[{"_id":"JiFr"}],"_id":"8271","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["16742052"],"eissn":["17529867"]},"issue":"9","volume":13,"oa_version":"None","pmid":1,"intvolume":" 13","month":"09","scopus_import":"1"},{"isi":1,"has_accepted_license":"1","year":"2020","day":"17","publication":"Physical Review Materials","date_published":"2020-08-17T00:00:00Z","doi":"10.1103/PhysRevMaterials.4.082602","date_created":"2020-07-07T11:33:54Z","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"citation":{"short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Grosjean","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425"},{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald","full_name":"Wald, Sebastian"},{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"}],"external_id":{"isi":["000561897000001"],"arxiv":["2006.07120"]},"article_processing_charge":"Yes","title":"Quantitatively consistent scale-spanning model for same-material tribocharging","article_number":"082602","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2475-9953"]},"publication_status":"published","file":[{"file_size":853753,"date_updated":"2020-08-17T15:54:20Z","creator":"ggrosjea","file_name":"Grosjean2020.pdf","date_created":"2020-08-17T15:54:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"288fef1eeb6540c6344bb8f7c8159dc9","file_id":"8277"}],"language":[{"iso":"eng"}],"volume":4,"related_material":{"record":[{"relation":"popular_science","status":"public","id":"12697"}]},"issue":"8","ec_funded":1,"abstract":[{"text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 4","date_updated":"2023-08-22T08:41:32Z","ddc":["530"],"department":[{"_id":"ScWa"}],"file_date_updated":"2020-08-17T15:54:20Z","_id":"8101","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"]},{"volume":378,"issue":"9","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00103616"],"eissn":["14320916"]},"publication_status":"published","month":"09","intvolume":" 378","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. "}],"department":[{"_id":"TaHa"}],"date_updated":"2023-08-22T09:00:03Z","status":"public","type":"journal_article","article_type":"original","_id":"8325","doi":"10.1007/s00220-020-03828-8","date_published":"2020-09-01T00:00:00Z","date_created":"2020-08-30T22:01:13Z","page":"1649-1675","day":"01","publication":"Communications in Mathematical Physics","isi":1,"year":"2020","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","title":"Sandpile solitons via smoothing of superharmonic functions","author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"}],"external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8318","department":[{"_id":"LeSa"}],"file_date_updated":"2020-08-31T13:40:00Z","ddc":["570"],"date_updated":"2023-08-22T09:03:00Z","month":"08","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I."}],"volume":11,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"1","file":[{"creator":"cziletti","file_size":7527373,"date_updated":"2020-08-31T13:40:00Z","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","date_created":"2020-08-31T13:40:00Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8326","checksum":"52b96f41d7d0db9728064c08da00d030"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","article_number":"4135","title":"Key role of quinone in the mechanism of respiratory complex I","author":[{"full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez","first_name":"Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol"},{"first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S.","last_name":"Minhas"},{"first_name":"Rozbeh","full_name":"Baradaran, Rozbeh","last_name":"Baradaran"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","first_name":"Margherita","last_name":"Tambalo","full_name":"Tambalo, Margherita"},{"first_name":"David T.","last_name":"Gallagher","full_name":"Gallagher, David T."},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0."},"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","date_published":"2020-08-18T00:00:00Z","doi":"10.1038/s41467-020-17957-0","date_created":"2020-08-30T22:01:10Z","day":"18","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020"},{"date_published":"2020-08-19T00:00:00Z","doi":"10.1134/S0026893320040111","date_created":"2020-08-30T22:01:11Z","page":"475-484","day":"19","publication":"Molecular Biology","isi":1,"year":"2020","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","title":"Expanding the genetic code: Unnatural base pairs in biological systems","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"P. M.","full_name":"Kolosov, P. M.","last_name":"Kolosov"},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"first_name":"E. Z.","full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva"}],"article_processing_charge":"No","external_id":{"isi":["000562110300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111"},"volume":54,"related_material":{"record":[{"relation":"original","id":"8321","status":"public"}]},"issue":"4","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"publication_status":"published","month":"08","intvolume":" 54","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T09:01:03Z","status":"public","type":"journal_article","article_type":"original","_id":"8320"},{"quality_controlled":"1","publisher":"Russian Academy of Sciences","page":"531-541","doi":"10.31857/S0026898420040126","date_published":"2020-07-01T00:00:00Z","date_created":"2020-08-30T22:01:11Z","year":"2020","day":"01","publication":"Molekuliarnaia biologiia","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","full_name":"Vlasov, Petr"},{"last_name":"Kolosov","full_name":"Kolosov, P. M.","first_name":"P. M."},{"first_name":"E. Y.","full_name":"Shuvalova, E. Y.","last_name":"Shuvalova"},{"first_name":"T. V.","full_name":"Egorova, T. V.","last_name":"Egorova"},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"external_id":{"pmid":["32799218"]},"article_processing_charge":"No","title":"Expanding the genetic code: Unnatural base pairs in biological systems","citation":{"ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","scopus_import":"1","month":"07","intvolume":" 54","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"oa_version":"None","pmid":1,"volume":54,"related_material":{"record":[{"relation":"translation","status":"public","id":"8320"}]},"issue":"4","publication_identifier":{"issn":["00268984"]},"publication_status":"published","language":[{"iso":"rus"}],"type":"journal_article","article_type":"original","status":"public","_id":"8321","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T09:01:02Z"},{"article_processing_charge":"No","external_id":{"isi":["000561483500001"]},"author":[{"first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach","full_name":"Pach, János"}],"title":"A farewell to Ricky Pollack","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","page":"571-574","date_created":"2020-08-30T22:01:12Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1007/s00454-020-00237-5","year":"2020","isi":1,"publication":"Discrete and Computational Geometry","day":"01","type":"journal_article","article_type":"letter_note","status":"public","_id":"8323","department":[{"_id":"HeEd"}],"date_updated":"2023-08-22T09:05:04Z","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"scopus_import":"1","intvolume":" 64","month":"10","oa_version":"None","volume":64,"publication_status":"published","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"language":[{"iso":"eng"}]},{"ec_funded":1,"volume":11,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8357","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_NatureComm_Kubiasova.pdf","date_created":"2020-09-10T08:05:19Z","file_size":3455704,"date_updated":"2020-09-10T08:05:19Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"intvolume":" 11","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER."}],"file_date_updated":"2020-09-10T08:05:19Z","department":[{"_id":"EvBe"}],"ddc":["580"],"date_updated":"2023-08-22T09:09:06Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8336","date_created":"2020-09-06T22:01:12Z","doi":"10.1038/s41467-020-17949-0","date_published":"2020-08-27T00:00:00Z","publication":"Nature Communications","day":"27","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","article_processing_charge":"No","external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"author":[{"last_name":"Kubiasova","full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","first_name":"Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","full_name":"Šamajová, Olga","last_name":"Šamajová"},{"full_name":"Nisler, Jaroslav","last_name":"Nisler","first_name":"Jaroslav"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Plíhalová, Lucie","last_name":"Plíhalová","first_name":"Lucie"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavý","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter"},{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Zalabák, David","last_name":"Zalabák","first_name":"David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"first_name":"Petr","last_name":"Galuszka","full_name":"Galuszka, Petr"},{"full_name":"Šamaj, Jozef","last_name":"Šamaj","first_name":"Jozef"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"article_number":"4285"},{"title":"Cell-surface receptors enable perception of extracellular cytokinins","article_processing_charge":"No","external_id":{"isi":["000567931000001"]},"author":[{"first_name":"Ioanna","full_name":"Antoniadi, Ioanna","last_name":"Antoniadi"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"first_name":"Radim","full_name":"Simerský, Radim","last_name":"Simerský"},{"last_name":"Mik","full_name":"Mik, Václav","first_name":"Václav"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"first_name":"Eduardo","full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"first_name":"Lenka","full_name":"Plačková, Lenka","last_name":"Plačková"},{"full_name":"Opassathian, Korawit","last_name":"Opassathian","first_name":"Korawit"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"first_name":"Colin","full_name":"Turnbull, Colin","last_name":"Turnbull"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9."},"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_number":"4284","date_created":"2020-09-06T22:01:13Z","date_published":"2020-08-27T00:00:00Z","doi":"10.1038/s41467-020-17700-9","publication":"Nature Communications","day":"27","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","file_date_updated":"2020-12-10T12:23:56Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-08-22T09:10:32Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8337","ec_funded":1,"volume":11,"language":[{"iso":"eng"}],"file":[{"date_created":"2020-12-10T12:23:56Z","file_name":"2020_NatureComm_Antoniadi.pdf","date_updated":"2020-12-10T12:23:56Z","file_size":3526415,"creator":"dernst","checksum":"5b96f39b598de7510cfefefb819b9a6d","file_id":"8936","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"intvolume":" 11","month":"08","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses."}]},{"article_processing_charge":"No","author":[{"last_name":"Varzi","full_name":"Varzi, Alberto","first_name":"Alberto"},{"first_name":"Katharina","full_name":"Thanner, Katharina","last_name":"Thanner"},{"first_name":"Roberto","last_name":"Scipioni","full_name":"Scipioni, Roberto"},{"first_name":"Daniele","last_name":"Di Lecce","full_name":"Di Lecce, Daniele"},{"first_name":"Jusef","full_name":"Hassoun, Jusef","last_name":"Hassoun"},{"first_name":"Susanne","last_name":"Dörfler","full_name":"Dörfler, Susanne"},{"first_name":"Holger","last_name":"Altheus","full_name":"Altheus, Holger"},{"first_name":"Stefan","last_name":"Kaskel","full_name":"Kaskel, Stefan"},{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"title":"Current status and future perspectives of Lithium metal batteries","citation":{"ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p.","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067.","ama":"Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d.","ieee":"A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria.","mla":"Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"IST Austria","page":"63","date_created":"2020-06-30T07:37:39Z","date_published":"2020-07-01T00:00:00Z","doi":"10.15479/AT:ISTA:8067","year":"2020","has_accepted_license":"1","day":"01","type":"technical_report","keyword":["Battery","Lithium metal","Lithium-sulphur","Lithium-air","All-solid-state"],"status":"public","_id":"8067","file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"StFr"}],"date_updated":"2023-08-22T09:20:36Z","ddc":["540"],"alternative_title":["IST Austria Technical Report"],"month":"07","abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"8361","relation":"later_version"}]},"publication_status":"submitted","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8076","checksum":"d183ca1465a1cbb4f8db27875cd156f7","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-02T07:36:04Z","file_name":"20200612_JPS_review_Li_metal_submitted.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:08Z","file_size":2612498}]},{"day":"31","publication":"Journal of Power Sources","isi":1,"year":"2020","date_published":"2020-12-31T00:00:00Z","doi":"10.1016/j.jpowsour.2020.228803","date_created":"2020-09-10T10:48:40Z","acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803.","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020).","ieee":"A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803","mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803."},"title":"Current status and future perspectives of lithium metal batteries","author":[{"first_name":"Alberto","last_name":"Varzi","orcid":"0000-0001-5069-0589","full_name":"Varzi, Alberto"},{"last_name":"Thanner","full_name":"Thanner, Katharina","orcid":"0000-0001-5394-2323","first_name":"Katharina"},{"last_name":"Scipioni","orcid":"0000-0003-1926-421X","full_name":"Scipioni, Roberto","first_name":"Roberto"},{"first_name":"Daniele","last_name":"Di Lecce","full_name":"Di Lecce, Daniele"},{"first_name":"Jusef","full_name":"Hassoun, Jusef","last_name":"Hassoun"},{"full_name":"Dörfler, Susanne","last_name":"Dörfler","first_name":"Susanne"},{"first_name":"Holger","last_name":"Altheus","full_name":"Altheus, Holger"},{"first_name":"Stefan","full_name":"Kaskel, Stefan","last_name":"Kaskel"},{"first_name":"Christian","orcid":"0000-0003-0654-0940","full_name":"Prehal, Christian","last_name":"Prehal"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"external_id":{"isi":["000593857300001"]},"article_processing_charge":"No","article_number":"228803","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0378-7753"]},"publication_status":"published","issue":"12","related_material":{"record":[{"id":"8067","status":"public","relation":"earlier_version"}]},"volume":480,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"month":"12","intvolume":" 480","main_file_link":[{"url":"https://doi.org/10.1016/j.jpowsour.2020.228803","open_access":"1"}],"date_updated":"2023-08-22T09:20:37Z","department":[{"_id":"StFr"}],"_id":"8361","status":"public","article_type":"original","type":"journal_article"},{"file_date_updated":"2020-09-18T13:02:37Z","department":[{"_id":"JoFi"}],"date_updated":"2023-08-22T09:27:12Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","_id":"8529","ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13056"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}]},"volume":11,"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8530","checksum":"88f92544889eb18bb38e25629a422a86","success":1,"date_updated":"2020-09-18T13:02:37Z","file_size":1002818,"creator":"dernst","date_created":"2020-09-18T13:02:37Z","file_name":"2020_NatureComm_Arnold.pdf"}],"intvolume":" 11","month":"09","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000577280200001"]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","citation":{"chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"article_number":"4460","date_created":"2020-09-18T10:56:20Z","doi":"10.1038/s41467-020-18269-z","date_published":"2020-09-08T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"08","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET)."},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"08","date_created":"2020-09-20T22:01:37Z","date_published":"2020-07-08T00:00:00Z","doi":"10.1145/3386569.3392466","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","citation":{"mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000583700300038"]},"author":[{"full_name":"Skrivan, Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Andreas","last_name":"Soderstrom","full_name":"Soderstrom, Andreas"},{"full_name":"Johansson, John","last_name":"Johansson","first_name":"John"},{"last_name":"Sprenger","full_name":"Sprenger, Christoph","first_name":"Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","article_number":"65","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_id":"8541","creator":"dernst","file_size":20223953,"date_updated":"2020-09-21T07:51:44Z","file_name":"2020_ACM_Skrivan.pdf","date_created":"2020-09-21T07:51:44Z"}],"ec_funded":1,"volume":39,"issue":"4","abstract":[{"lang":"eng","text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 39","month":"07","date_updated":"2023-08-22T09:28:27Z","ddc":["000"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-09-21T07:51:44Z","_id":"8535","article_type":"original","type":"journal_article","status":"public"},{"external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"article_processing_charge":"No","author":[{"full_name":"Su, C.","last_name":"Su","first_name":"C."},{"last_name":"Zhao","full_name":"Zhao, Gufang","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhong","full_name":"Zhong, C.","first_name":"C."}],"title":"On the K-theory stable bases of the springer resolution","citation":{"mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431","apa":"Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"663-671","date_created":"2020-09-20T22:01:38Z","date_published":"2020-06-01T00:00:00Z","doi":"10.24033/asens.2431","year":"2020","isi":1,"publication":"Annales Scientifiques de l'Ecole Normale Superieure","day":"01","oa":1,"publisher":"Société Mathématique de France","quality_controlled":"1","department":[{"_id":"TaHa"}],"date_updated":"2023-08-22T09:27:57Z","article_type":"original","type":"journal_article","status":"public","_id":"8539","volume":53,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0012-9593"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.08013","open_access":"1"}],"scopus_import":"1","intvolume":" 53","month":"06","abstract":[{"text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.","lang":"eng"},{"lang":"fre","text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. "}],"oa_version":"Preprint"},{"year":"2020","day":"27","date_created":"2023-05-23T13:37:41Z","doi":"10.5281/ZENODO.3961561","date_published":"2020-07-27T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"abstract":[{"text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3961562"}],"publisher":"Zenodo","month":"07","date_updated":"2023-08-22T09:27:11Z","citation":{"ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561."},"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","department":[{"_id":"JoFi"}],"_id":"13056","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8579","department":[{"_id":"LeSa"}],"file_date_updated":"2020-09-28T11:36:50Z","date_updated":"2023-08-22T09:34:06Z","ddc":["570"],"scopus_import":"1","intvolume":" 10","month":"09","abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"oa_version":"Published Version","issue":"9","volume":10,"publication_status":"published","publication_identifier":{"eissn":["20770375"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8583","checksum":"ceb43d7554e712dea6f36f9287271737","file_size":4612258,"date_updated":"2020-09-28T11:36:50Z","creator":"dernst","file_name":"2020_Membranes_Andrei.pdf","date_created":"2020-09-28T11:36:50Z"}],"article_number":"242","external_id":{"isi":["000581446000001"]},"article_processing_charge":"No","author":[{"full_name":"Andrei, Andreea","last_name":"Andrei","first_name":"Andreea"},{"first_name":"Yavuz","last_name":"Öztürk","full_name":"Öztürk, Yavuz"},{"last_name":"Khalfaoui-Hassani","full_name":"Khalfaoui-Hassani, Bahia","first_name":"Bahia"},{"last_name":"Rauch","full_name":"Rauch, Juna","first_name":"Juna"},{"last_name":"Marckmann","full_name":"Marckmann, Dorian","first_name":"Dorian"},{"first_name":"Petru Iulian","id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Trasnea, Petru Iulian","last_name":"Trasnea"},{"first_name":"Fevzi","last_name":"Daldal","full_name":"Daldal, Fevzi"},{"first_name":"Hans-Georg","last_name":"Koch","full_name":"Koch, Hans-Georg"}],"title":"Cu homeostasis in bacteria: The ins and outs","citation":{"mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.","ieee":"A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"MDPI","date_created":"2020-09-28T08:59:26Z","date_published":"2020-09-01T00:00:00Z","doi":"10.3390/membranes10090242","year":"2020","isi":1,"has_accepted_license":"1","publication":"Membranes","day":"01"},{"scopus_import":"1","intvolume":" 27","month":"11","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"abstract":[{"text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.","lang":"eng"}],"oa_version":"None","pmid":1,"issue":"11","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/","description":"News on IST Homepage"}]},"volume":27,"publication_status":"published","publication_identifier":{"issn":["15459993"],"eissn":["15459985"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"8581","department":[{"_id":"LeSa"}],"date_updated":"2023-08-22T09:33:09Z","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission.","page":"1077-1085","date_created":"2020-09-28T08:59:27Z","doi":"10.1038/s41594-020-0503-8","date_published":"2020-11-01T00:00:00Z","year":"2020","isi":1,"publication":"Nature Structural and Molecular Biology","day":"01","article_processing_charge":"No","external_id":{"isi":["000569299400004"],"pmid":["32929284"]},"author":[{"full_name":"Pinke, Gergely","last_name":"Pinke","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"last_name":"Zhou","full_name":"Zhou, Long","orcid":"0000-0002-1864-8951","first_name":"Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","citation":{"ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.","chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.","apa":"Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-020-0503-8","ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085. doi:10.1038/s41594-020-0503-8","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020.","mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"status":"public","type":"conference","conference":{"start_date":"2020-07-15","end_date":"2020-07-15","location":"Pisa, Italy","name":"ESGCO: European Study Group on Cardiovascular Oscillations"},"article_number":"9158054","_id":"8580","department":[{"_id":"HeEd"}],"title":"The application of persistent homology in the analysis of heart rate variability","author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"first_name":"Beata","last_name":"Graff","full_name":"Graff, Beata"},{"last_name":"Jablonski","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"article_processing_charge":"No","external_id":{"isi":["000621172600045"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.","short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.","apa":"Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054","chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054."},"date_updated":"2023-08-22T09:33:34Z","month":"08","publisher":"IEEE","scopus_import":"1","quality_controlled":"1","oa_version":"None","abstract":[{"text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.","lang":"eng"}],"date_published":"2020-08-01T00:00:00Z","doi":"10.1109/ESGCO49734.2020.9158054","date_created":"2020-09-28T08:59:27Z","day":"01","publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728157511"]},"isi":1,"publication_status":"published","year":"2020"},{"ddc":["570"],"date_updated":"2023-08-22T09:53:01Z","department":[{"_id":"SiHi"}],"file_date_updated":"2020-12-10T14:07:24Z","_id":"8592","status":"public","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8938","checksum":"92818c23ecc70e35acfa671f3cfb9909","file_size":7835833,"date_updated":"2020-12-10T14:07:24Z","creator":"dernst","file_name":"2020_AdvScience_Tian.pdf","date_created":"2020-12-10T14:07:24Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2198-3844"]},"publication_status":"published","issue":"21","volume":7,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma."}],"month":"11","intvolume":" 7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724."},"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","author":[{"last_name":"Tian","full_name":"Tian, Anhao","first_name":"Anhao"},{"first_name":"Bo","full_name":"Kang, Bo","last_name":"Kang"},{"full_name":"Li, Baizhou","last_name":"Li","first_name":"Baizhou"},{"first_name":"Biying","last_name":"Qiu","full_name":"Qiu, Biying"},{"first_name":"Wenhong","full_name":"Jiang, Wenhong","last_name":"Jiang"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"first_name":"Qingqing","full_name":"Gao, Qingqing","last_name":"Gao"},{"last_name":"Liu","full_name":"Liu, Rui","first_name":"Rui"},{"first_name":"Chengwei","last_name":"Cai","full_name":"Cai, Chengwei"},{"last_name":"Jing","full_name":"Jing, Rui","first_name":"Rui"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"last_name":"Chen","full_name":"Chen, Pengxiang","first_name":"Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"first_name":"Lili","full_name":"Bao, Lili","last_name":"Bao"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"full_name":"Wang, Yan","last_name":"Wang","first_name":"Yan"},{"full_name":"Shi, Yu","last_name":"Shi","first_name":"Yu"},{"last_name":"Li","full_name":"Li, Jin","first_name":"Jin"},{"first_name":"Minmin","full_name":"Yang, Minmin","last_name":"Yang"},{"first_name":"Lisha","full_name":"Wang, Lisha","last_name":"Wang"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"last_name":"Bian","full_name":"Bian, Xiuwu","first_name":"Xiuwu"},{"last_name":"Wang","full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie"},{"first_name":"Chong","last_name":"Liu","full_name":"Liu, Chong"}],"external_id":{"isi":["000573860700001"]},"article_processing_charge":"No","article_number":"2001724","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"day":"04","publication":"Advanced Science","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1002/advs.202001724","date_published":"2020-11-04T00:00:00Z","date_created":"2020-10-01T09:44:13Z","acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","quality_controlled":"1","publisher":"Wiley","oa":1},{"month":"09","intvolume":" 11","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"volume":11,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"file":[{"date_created":"2020-09-28T13:16:15Z","file_name":"2020_NatureComm_Prehal.pdf","creator":"dernst","date_updated":"2020-09-28T13:16:15Z","file_size":1822469,"checksum":"eada7bc8dd16a49390137cff882ef328","file_id":"8585","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8568","department":[{"_id":"StFr"}],"file_date_updated":"2020-09-28T13:16:15Z","ddc":["530"],"date_updated":"2023-08-22T09:37:24Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s41467-020-18610-6","date_published":"2020-09-24T00:00:00Z","date_created":"2020-09-25T07:23:13Z","day":"24","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020","article_number":"4838","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"last_name":"Fitzek","full_name":"Fitzek, Harald","first_name":"Harald"},{"full_name":"Kothleitner, Gerald","last_name":"Kothleitner","first_name":"Gerald"},{"first_name":"Volker","full_name":"Presser, Volker","last_name":"Presser"},{"first_name":"Bernhard","last_name":"Gollas","full_name":"Gollas, Bernhard"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Abbas, Qamar","last_name":"Abbas","first_name":"Qamar"}],"external_id":{"isi":["000573756600004"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6."}},{"file_date_updated":"2020-10-12T12:39:10Z","department":[{"_id":"MaJö"}],"ddc":["570"],"date_updated":"2023-08-22T09:58:21Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8643","volume":10,"file":[{"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","file_id":"8651","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-12T12:39:10Z","file_name":"2020_ScientificReport_Deichler.pdf","creator":"dernst","date_updated":"2020-10-12T12:39:10Z","file_size":3906744}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","month":"10","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}],"title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","author":[{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"full_name":"Carrasco, Denisse","last_name":"Carrasco","first_name":"Denisse"},{"first_name":"Luciana","full_name":"Lopez-Jury, Luciana","last_name":"Lopez-Jury"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marquez, Natalia","last_name":"Marquez","first_name":"Natalia"},{"last_name":"Mpodozis","full_name":"Mpodozis, Jorge","first_name":"Jorge"},{"last_name":"Marin","full_name":"Marin, Gonzalo","first_name":"Gonzalo"}],"article_processing_charge":"No","external_id":{"isi":["000577142600032"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0."},"article_number":"16220","date_published":"2020-10-01T00:00:00Z","doi":"10.1038/s41598-020-72848-0","date_created":"2020-10-11T22:01:14Z","day":"01","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.)."},{"page":"1960-1962","date_created":"2020-10-11T22:01:14Z","doi":"10.1093/bioinformatics/btz841","date_published":"2020-03-15T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Bioinformatics","day":"15","oa":1,"quality_controlled":"1","publisher":"Oxford Academic","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","article_processing_charge":"No","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"author":[{"first_name":"Laura A","full_name":"Esteban, Laura A","last_name":"Esteban"},{"last_name":"Lonishin","full_name":"Lonishin, Lyubov R","first_name":"Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"full_name":"Leleytner, Gregory","last_name":"Leleytner","first_name":"Gregory"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N ","last_name":"Ivankov"}],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","citation":{"mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"ec_funded":1,"issue":"6","volume":36,"publication_status":"published","publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":308341,"date_updated":"2020-10-12T12:02:09Z","file_name":"2020_Bioinformatics_Esteban.pdf","date_created":"2020-10-12T12:02:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"21d6f71839deb3b83e4a356193f72767","file_id":"8649"}],"scopus_import":"1","intvolume":" 36","month":"03","abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"FyKo"}],"file_date_updated":"2020-10-12T12:02:09Z","date_updated":"2023-08-22T09:57:29Z","ddc":["000","570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8645"},{"abstract":[{"text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 17","month":"09","publication_status":"published","publication_identifier":{"eissn":["14783975"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fec9bdd355ed349f09990faab20838a7","file_id":"8609","success":1,"date_updated":"2020-10-05T13:53:59Z","file_size":1667111,"creator":"dernst","date_created":"2020-10-05T13:53:59Z","file_name":"2020_PhysBio_Merrin.pdf"}],"volume":17,"issue":"6","_id":"8597","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T09:53:29Z","ddc":["510","570"],"department":[{"_id":"NanoFab"}],"file_date_updated":"2020-10-05T13:53:59Z","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"Physical Biology","day":"23","date_created":"2020-10-04T22:01:35Z","doi":"10.1088/1478-3975/abb2db","date_published":"2020-09-23T00:00:00Z","article_number":"065005","citation":{"chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db.","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","short":"J. Merrin, Physical Biology 17 (2020).","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db","ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000575539700001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"}],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide"}]