[{"date_updated":"2023-08-03T14:11:29Z","day":"29","citation":{"ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022."},"month":"12","date_created":"2023-01-08T23:00:53Z","date_published":"2022-12-29T00:00:00Z","article_type":"original","volume":6,"intvolume":"         6","publication":"Physical Review Materials","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"quality_controlled":"1","issue":"12","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix","last_name":"Pertl","first_name":"Felix"},{"last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050","last_name":"Shafeek","first_name":"Lubuna B"},{"last_name":"Cramer","first_name":"Tobias","full_name":"Cramer, Tobias"},{"last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"status":"public","article_number":"125605","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","scopus_import":"1","type":"journal_article","year":"2022","isi":1,"arxiv":1,"oa_version":"Preprint","doi":"10.1103/PhysRevMaterials.6.125605","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"12109","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","article_processing_charge":"No","publication_identifier":{"eissn":["2475-9953"]},"ec_funded":1,"abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}]},{"quality_controlled":"1","publisher":"AIP Publishing","publication":"Journal of Mathematical Physics","intvolume":"        63","issue":"12","oa":1,"author":[{"full_name":"Henheik, Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","last_name":"Henheik","orcid":"0000-0003-1106-327X"},{"last_name":"Tumulka","first_name":"Roderich","full_name":"Tumulka, Roderich"}],"title":"Interior-boundary conditions for the Dirac equation at point sources in three dimensions","article_number":"122302","status":"public","citation":{"ista":"Henheik SJ, Tumulka R. 2022. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. Journal of Mathematical Physics. 63(12), 122302.","ama":"Henheik SJ, Tumulka R. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. 2022;63(12). doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12, 122302, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>.","chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>.","apa":"Henheik, S. J., &#38; Tumulka, R. (2022). Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>","short":"S.J. Henheik, R. Tumulka, Journal of Mathematical Physics 63 (2022).","ieee":"S. J. Henheik and R. Tumulka, “Interior-boundary conditions for the Dirac equation at point sources in three dimensions,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12. AIP Publishing, 2022."},"day":"01","file":[{"date_created":"2023-01-20T11:58:59Z","file_size":5436804,"file_id":"12327","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_name":"2022_JourMathPhysics_Henheik.pdf","success":1,"date_updated":"2023-01-20T11:58:59Z","checksum":"5150287295e0ce4f12462c990744d65d"}],"date_updated":"2023-08-03T14:12:01Z","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2023-01-08T23:00:53Z","date_published":"2022-12-01T00:00:00Z","month":"12","has_accepted_license":"1","volume":63,"article_type":"original","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"external_id":{"isi":["000900748900002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LaEr"}],"_id":"12110","language":[{"iso":"eng"}],"ddc":["510"],"publication_status":"published","file_date_updated":"2023-01-20T11:58:59Z","publication_identifier":{"issn":["0022-2488"]},"acknowledgement":"J.H. gratefully acknowledges the partial financial support by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331.\r\n","article_processing_charge":"No","abstract":[{"lang":"eng","text":"A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, i.e., for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has successfully been done already in one space dimension, and more generally for codimension-1 boundaries, the situation of point sources in three dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3D, which also correspond to a boundary condition. Indeed, we confirm this expectation here by proving that there is no self-adjoint operator on a (truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with an IBC (on the boundary consisting of configurations with a particle at the origin) that are away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential."}],"ec_funded":1,"isi":1,"type":"journal_article","year":"2022","scopus_import":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1063/5.0104675"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"_id":"12111","ddc":["530"],"publication_status":"published","acknowledgement":"We thank G. Blatter, T. Ihn, K. Ensslin, M. Goldstein, C. Carisch, and J. del Pino for illuminating discussions and acknowledge financial support from the Swiss National Science Foundation (SNSF) through Project No. 190078, and from the Deutsche Forschungsgemeinschaft (DFG) - Project No. 449653034. Our numerical implementations are based on the ITensors JULIA library [64].","article_processing_charge":"No","file_date_updated":"2023-01-20T12:03:31Z","publication_identifier":{"issn":["2643-1564"]},"abstract":[{"lang":"eng","text":"Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up."}],"type":"journal_article","year":"2022","scopus_import":"1","oa_version":"Published Version","doi":"10.1103/PhysRevResearch.4.043177","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Physical Review Research","intvolume":"         4","quality_controlled":"1","publisher":"American Physical Society","issue":"4","author":[{"full_name":"Stocker, Lidia","first_name":"Lidia","last_name":"Stocker"},{"first_name":"Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan"},{"full_name":"Ferguson, Michael S.","last_name":"Ferguson","first_name":"Michael S."},{"last_name":"Zilberberg","first_name":"Oded","full_name":"Zilberberg, Oded"}],"oa":1,"status":"public","title":"Entanglement-based observables for quantum impurities","article_number":"043177","date_updated":"2023-02-13T09:08:28Z","day":"01","citation":{"ama":"Stocker L, Sack S, Ferguson MS, Zilberberg O. Entanglement-based observables for quantum impurities. <i>Physical Review Research</i>. 2022;4(4). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">10.1103/PhysRevResearch.4.043177</a>","ista":"Stocker L, Sack S, Ferguson MS, Zilberberg O. 2022. Entanglement-based observables for quantum impurities. Physical Review Research. 4(4), 043177.","mla":"Stocker, Lidia, et al. “Entanglement-Based Observables for Quantum Impurities.” <i>Physical Review Research</i>, vol. 4, no. 4, 043177, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">10.1103/PhysRevResearch.4.043177</a>.","chicago":"Stocker, Lidia, Stefan Sack, Michael S. Ferguson, and Oded Zilberberg. “Entanglement-Based Observables for Quantum Impurities.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">https://doi.org/10.1103/PhysRevResearch.4.043177</a>.","short":"L. Stocker, S. Sack, M.S. Ferguson, O. Zilberberg, Physical Review Research 4 (2022).","apa":"Stocker, L., Sack, S., Ferguson, M. S., &#38; Zilberberg, O. (2022). Entanglement-based observables for quantum impurities. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">https://doi.org/10.1103/PhysRevResearch.4.043177</a>","ieee":"L. Stocker, S. Sack, M. S. Ferguson, and O. Zilberberg, “Entanglement-based observables for quantum impurities,” <i>Physical Review Research</i>, vol. 4, no. 4. American Physical Society, 2022."},"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"12328","relation":"main_file","file_size":2941167,"date_created":"2023-01-20T12:03:31Z","checksum":"556820cf6e4af77c8476e5b8f4114d1a","date_updated":"2023-01-20T12:03:31Z","success":1,"file_name":"2022_PhysicalReviewResearch_Stocker.pdf"}],"month":"12","date_created":"2023-01-08T23:00:53Z","date_published":"2022-12-01T00:00:00Z","article_type":"original","volume":4,"has_accepted_license":"1"},{"article_type":"letter_note","volume":378,"month":"12","date_published":"2022-12-22T00:00:00Z","date_created":"2023-01-12T11:56:30Z","date_updated":"2023-10-03T11:01:06Z","citation":{"short":"K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.","apa":"Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>","ieee":"K. Chhugani <i>et al.</i>, “Remote opportunities for scholars in Ukraine,” <i>Science</i>, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022.","chicago":"Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>.","ista":"Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars in Ukraine. Science. 378(6626), 1285–1286.","ama":"Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. <i>Science</i>. 2022;378(6626):1285-1286. doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>","mla":"Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>."},"day":"22","status":"public","title":"Remote opportunities for scholars in Ukraine","author":[{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"last_name":"Frolova","first_name":"Alina","full_name":"Frolova, Alina"},{"last_name":"Salyha","first_name":"Yuriy","full_name":"Salyha, Yuriy"},{"full_name":"Fiscutean, Andrada","first_name":"Andrada","last_name":"Fiscutean"},{"first_name":"Oksana","last_name":"Zlenko","full_name":"Zlenko, Oksana"},{"last_name":"Reinsone","first_name":"Sanita","full_name":"Reinsone, Sanita"},{"first_name":"Walter W.","last_name":"Wolfsberger","full_name":"Wolfsberger, Walter W."},{"full_name":"Ivashchenko, Oleksandra V.","first_name":"Oleksandra V.","last_name":"Ivashchenko"},{"last_name":"Maci","first_name":"Megi","full_name":"Maci, Megi"},{"last_name":"Dziuba","first_name":"Dmytro","full_name":"Dziuba, Dmytro"},{"first_name":"Andrii","last_name":"Parkhomenko","full_name":"Parkhomenko, Andrii"},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Łabaj","first_name":"Paweł P.","full_name":"Łabaj, Paweł P."},{"full_name":"Romero, Veronika","first_name":"Veronika","last_name":"Romero"},{"last_name":"Hlávka","first_name":"Jakub","full_name":"Hlávka, Jakub"},{"full_name":"Oleksyk, Taras K.","first_name":"Taras K.","last_name":"Oleksyk"},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"}],"oa":1,"issue":"6626","intvolume":"       378","publication":"Science","publisher":"American Association for the Advancement of Science","page":"1285-1286","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1126/science.adg0797","open_access":"1"}],"doi":"10.1126/science.adg0797","oa_version":"Published Version","scopus_import":"1","year":"2022","type":"journal_article","isi":1,"abstract":[{"text":"Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.","lang":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"_id":"12116","department":[{"_id":"FyKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000963463700023"]}},{"scopus_import":"1","year":"2022","type":"journal_article","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"doi":"10.1016/j.xpro.2022.101866","oa_version":"Published Version","ddc":["570"],"publication_status":"published","_id":"12117","language":[{"iso":"eng"}],"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"},{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"ec_funded":1,"publication_identifier":{"issn":["2666-1667"]},"file_date_updated":"2023-01-23T09:50:51Z","article_processing_charge":"No","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","related_material":{"record":[{"status":"public","id":"11478","relation":"other"}]},"file":[{"date_updated":"2023-01-23T09:50:51Z","success":1,"file_name":"2022_STARProtocols_Huebschmann.pdf","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_size":6251945,"file_id":"12340","creator":"dernst","relation":"main_file","date_created":"2023-01-23T09:50:51Z","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>.","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022."},"day":"16","date_updated":"2023-11-02T12:21:32Z","has_accepted_license":"1","article_type":"letter_note","volume":3,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2022-12-16T00:00:00Z","date_created":"2023-01-12T11:56:38Z","month":"12","issue":"4","acknowledged_ssus":[{"_id":"Bio"}],"publisher":"Elsevier","quality_controlled":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"intvolume":"         3","publication":"STAR Protocols","article_number":"101866","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","status":"public","oa":1,"author":[{"last_name":"Hübschmann","first_name":"Verena","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korkut","orcid":"0000-0003-4309-2251","first_name":"Medina","full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}]},{"keyword":["Multidisciplinary"],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2203.07829","open_access":"1"}],"page":"442-447","quality_controlled":"1","publisher":"Springer Nature","publication":"Nature","intvolume":"       612","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"issue":"7940","oa":1,"author":[{"full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini"},{"first_name":"Maksim","last_name":"Borovkov","full_name":"Borovkov, Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"last_name":"Prada","first_name":"Elsa","full_name":"Prada, Elsa"},{"full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez","first_name":"Sara"},{"full_name":"Botifoll, Marc","first_name":"Marc","last_name":"Botifoll"},{"first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Aguado, Ramón","last_name":"Aguado","first_name":"Ramón"},{"full_name":"San-Jose, Pablo","first_name":"Pablo","last_name":"San-Jose"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"title":"Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks","status":"public","citation":{"apa":"Valentini, M., Borovkov, M., Prada, E., Martí-Sánchez, S., Botifoll, M., Hofmann, A. C., … Katsaros, G. (2022). Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>","short":"M. Valentini, M. Borovkov, E. Prada, S. Martí-Sánchez, M. Botifoll, A.C. Hofmann, J. Arbiol, R. Aguado, P. San-Jose, G. Katsaros, Nature 612 (2022) 442–447.","ieee":"M. Valentini <i>et al.</i>, “Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks,” <i>Nature</i>, vol. 612, no. 7940. Springer Nature, pp. 442–447, 2022.","ista":"Valentini M, Borovkov M, Prada E, Martí-Sánchez S, Botifoll M, Hofmann AC, Arbiol J, Aguado R, San-Jose P, Katsaros G. 2022. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. Nature. 612(7940), 442–447.","ama":"Valentini M, Borovkov M, Prada E, et al. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. 2022;612(7940):442-447. doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>","mla":"Valentini, Marco, et al. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>, vol. 612, no. 7940, Springer Nature, 2022, pp. 442–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>.","chicago":"Valentini, Marco, Maksim Borovkov, Elsa Prada, Sara Martí-Sánchez, Marc Botifoll, Andrea C Hofmann, Jordi Arbiol, Ramón Aguado, Pablo San-Jose, and Georgios Katsaros. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>."},"day":"15","date_updated":"2024-02-21T12:35:33Z","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/imposter-particles-revealed-and-explained/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"13286","relation":"dissertation_contains"},{"id":"12522","relation":"research_data","status":"public"}]},"date_published":"2022-12-15T00:00:00Z","date_created":"2023-01-12T11:56:45Z","month":"12","article_type":"original","volume":612,"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"}],"external_id":{"isi":["000899725400001"],"arxiv":["2203.07829"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GeKa"}],"_id":"12118","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledgement":"We thank P. Krogstrup for providing us with the NW materials. We thank A. Higginbotham, E. J. H. Lee, C. Marcus and S. Vaitiekėnas for helpful discussions and G. Steffensen for his input on the diffusive Little-Parks theory. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation; the CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). A.H. acknowledges support from H2020-MSCA-IF-2018/844511. ICN2 also acknowledges funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa Program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. Authors acknowledge the use of instrumentation as well as the technical advice provided by the National Facility ELECMI ICTS, node ‘Laboratorio de Microscopías Avanzadas’ at University of Zaragoza. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 823717-ESTEEM3. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. This research is part of the CSIC programme for the Spanish Recovery, Transformation and Resilience Plan funded by the Recovery and Resilience Facility of the European Union, established by the Regulation (EU) 2020/2094. We thank support from Grant PGC2018-097018-BI00, project FlagERA TOPOGRAPH (PCI2018-093026) and project NANOGEN (PID2020-116093RB-C43), funded by MCIN/AEI/10.13039/501100011033/ and by ‘ERDF A way of making Europe’, by the European Union. M. Botifoll acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund (project ref. 2020 FI 00103).","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes."}],"ec_funded":1,"year":"2022","type":"journal_article","isi":1,"arxiv":1,"scopus_import":"1","oa_version":"Preprint","doi":"10.1038/s41586-022-05382-w"},{"language":[{"iso":"eng"}],"_id":"12119","publication_status":"published","ddc":["570"],"department":[{"_id":"MiSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"external_id":{"pmid":["36272416"],"isi":["000922019600003"]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events."}],"acknowledgement":"We thank Coung Kieu and Dominik van den Heuvel for excellent technical assistance. This work was supported by the German Research Foundation (PE2704/2-1, PE2704/3-1 to T.P., SFB 1123-project B06 to S.M., SFB1525 project A07 to D.S, TRR 332 project A7 to C.S., PO 2247/2-1 to A.P., SFB1116-project B11 to A.P. and B12 to M.K.), LMU Munich’s Institutional\r\nStrategy LMUexcellent within the framework of the German Excellence Initiative (No. 806 32 006 to T.P.), and by the German Centre for Cardiovascular Research (DZHK) to T.P. (Postdoc Start-up grant No. 100378833). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 833440 to S.M.). F.G. received funding from the European Union’s\r\nHorizon 2020 research and innovation program under the Marie Sk1odowska-Curie grant agreement no. 747687. A.H. was funded by RTI2018-095497-B-I00 from Ministerio de Ciencia e Innovacio´ n (MICINN), HR17_00527 from Fundacion La Caixa, and Transatlantic Network of Excellence (TNE-18CVD04) from the Leducq Foundation. The CNIC is supported by the MICINN and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (CEX2020-001041-S). A.P. was supported by the Forschungskommission of the Medical Faculty of the Heinrich-Heine-Universität Düsseldorf (No. 18-2019 to A.P.). C.G. was supported by the Helmholtz Alliance ‘Aging and Metabolic Programming, AMPro,’ by the German Federal\r\nMinistry of Education and Research to the German Center for Diabetes Research (DZD), and by the Bavarian State Ministry of Health and Care through the research project DigiMed Bayern.","article_processing_charge":"No","file_date_updated":"2023-01-23T10:18:48Z","publication_identifier":{"issn":["1074-7613"]},"type":"journal_article","year":"2022","isi":1,"scopus_import":"1","doi":"10.1016/j.immuni.2022.10.001","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"pmid":1,"oa_version":"Published Version","issue":"12","publication":"Immunity","intvolume":"        55","page":"2285-2299.e7","keyword":["Infectious Diseases","Immunology","Immunology and Allergy"],"quality_controlled":"1","publisher":"Elsevier","status":"public","title":"Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease","author":[{"full_name":"Petzold, Tobias","first_name":"Tobias","last_name":"Petzold"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"last_name":"Ballesteros","first_name":"Iván","full_name":"Ballesteros, Iván"},{"full_name":"Saleh, Inas","last_name":"Saleh","first_name":"Inas"},{"full_name":"Polzin, Amin","first_name":"Amin","last_name":"Polzin"},{"full_name":"Thienel, Manuela","first_name":"Manuela","last_name":"Thienel"},{"full_name":"Liu, Lulu","last_name":"Liu","first_name":"Lulu"},{"full_name":"Ul Ain, Qurrat","first_name":"Qurrat","last_name":"Ul Ain"},{"last_name":"Ehreiser","first_name":"Vincent","full_name":"Ehreiser, Vincent"},{"full_name":"Weber, Christian","first_name":"Christian","last_name":"Weber"},{"full_name":"Kilani, Badr","first_name":"Badr","last_name":"Kilani"},{"last_name":"Mertsch","first_name":"Pontus","full_name":"Mertsch, Pontus"},{"first_name":"Jeremias","last_name":"Götschke","full_name":"Götschke, Jeremias"},{"last_name":"Cremer","first_name":"Sophie","full_name":"Cremer, Sophie"},{"first_name":"Wenwen","last_name":"Fu","full_name":"Fu, Wenwen"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"first_name":"Hellen","last_name":"Ishikawa-Ankerhold","full_name":"Ishikawa-Ankerhold, Hellen"},{"last_name":"Raatz","first_name":"Elisabeth","full_name":"Raatz, Elisabeth"},{"last_name":"El-Nemr","first_name":"Shaza","full_name":"El-Nemr, Shaza"},{"first_name":"Agnes","last_name":"Görlach","full_name":"Görlach, Agnes"},{"full_name":"Marhuenda, Esther","last_name":"Marhuenda","first_name":"Esther"},{"last_name":"Stark","first_name":"Konstantin","full_name":"Stark, Konstantin"},{"last_name":"Pircher","first_name":"Joachim","full_name":"Pircher, Joachim"},{"last_name":"Stegner","first_name":"David","full_name":"Stegner, David"},{"last_name":"Gieger","first_name":"Christian","full_name":"Gieger, Christian"},{"full_name":"Schmidt-Supprian, Marc","last_name":"Schmidt-Supprian","first_name":"Marc"},{"first_name":"Florian R","orcid":"0000-0001-6120-3723","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"},{"full_name":"Almendros, Isaac","first_name":"Isaac","last_name":"Almendros"},{"full_name":"Kelm, Malte","first_name":"Malte","last_name":"Kelm"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"first_name":"Andrés","last_name":"Hidalgo","full_name":"Hidalgo, Andrés"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"oa":1,"date_updated":"2023-08-03T14:21:51Z","day":"13","citation":{"ieee":"T. Petzold <i>et al.</i>, “Neutrophil ‘plucking’ on megakaryocytes drives platelet production and boosts cardiovascular disease,” <i>Immunity</i>, vol. 55, no. 12. Elsevier, p. 2285–2299.e7, 2022.","short":"T. Petzold, Z. Zhang, I. Ballesteros, I. Saleh, A. Polzin, M. Thienel, L. Liu, Q. Ul Ain, V. Ehreiser, C. Weber, B. Kilani, P. Mertsch, J. Götschke, S. Cremer, W. Fu, M. Lorenz, H. Ishikawa-Ankerhold, E. Raatz, S. El-Nemr, A. Görlach, E. Marhuenda, K. Stark, J. Pircher, D. Stegner, C. Gieger, M. Schmidt-Supprian, F.R. Gärtner, I. Almendros, M. Kelm, C. Schulz, A. Hidalgo, S. Massberg, Immunity 55 (2022) 2285–2299.e7.","apa":"Petzold, T., Zhang, Z., Ballesteros, I., Saleh, I., Polzin, A., Thienel, M., … Massberg, S. (2022). Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">https://doi.org/10.1016/j.immuni.2022.10.001</a>","mla":"Petzold, Tobias, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” <i>Immunity</i>, vol. 55, no. 12, Elsevier, 2022, p. 2285–2299.e7, doi:<a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">10.1016/j.immuni.2022.10.001</a>.","ista":"Petzold T, Zhang Z, Ballesteros I, Saleh I, Polzin A, Thienel M, Liu L, Ul Ain Q, Ehreiser V, Weber C, Kilani B, Mertsch P, Götschke J, Cremer S, Fu W, Lorenz M, Ishikawa-Ankerhold H, Raatz E, El-Nemr S, Görlach A, Marhuenda E, Stark K, Pircher J, Stegner D, Gieger C, Schmidt-Supprian M, Gärtner FR, Almendros I, Kelm M, Schulz C, Hidalgo A, Massberg S. 2022. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. Immunity. 55(12), 2285–2299.e7.","ama":"Petzold T, Zhang Z, Ballesteros I, et al. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. <i>Immunity</i>. 2022;55(12):2285-2299.e7. doi:<a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">10.1016/j.immuni.2022.10.001</a>","chicago":"Petzold, Tobias, Zhe Zhang, Iván Ballesteros, Inas Saleh, Amin Polzin, Manuela Thienel, Lulu Liu, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” <i>Immunity</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">https://doi.org/10.1016/j.immuni.2022.10.001</a>."},"file":[{"file_name":"2022_Immunity_Petzold.pdf","success":1,"date_updated":"2023-01-23T10:18:48Z","checksum":"073267a9c0ad9f85a650053bc7b23777","date_created":"2023-01-23T10:18:48Z","file_size":5299475,"creator":"dernst","relation":"main_file","file_id":"12341","access_level":"open_access","content_type":"application/pdf"}],"volume":55,"article_type":"original","has_accepted_license":"1","month":"12","date_created":"2023-01-12T11:56:54Z","date_published":"2022-12-13T00:00:00Z"},{"publication_status":"published","_id":"12120","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000919603800005"],"pmid":["36473460"]},"abstract":[{"lang":"eng","text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth."}],"article_processing_charge":"No","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","publication_identifier":{"issn":["1534-5807"]},"scopus_import":"1","isi":1,"year":"2022","type":"journal_article","doi":"10.1016/j.devcel.2022.11.006","pmid":1,"oa_version":"None","issue":"23","intvolume":"        57","publication":"Developmental Cell","publisher":"Elsevier","page":"2638-2651.e6","quality_controlled":"1","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"status":"public","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","author":[{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"first_name":"Yumei","last_name":"Hu","full_name":"Hu, Yumei"},{"last_name":"Wang","first_name":"Yaping","full_name":"Wang, Yaping"},{"first_name":"Jinkui","last_name":"Cheng","full_name":"Cheng, Jinkui"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"last_name":"Chen","first_name":"Guojingwei","full_name":"Chen, Guojingwei"},{"first_name":"Qian","last_name":"Li","full_name":"Li, Qian"},{"last_name":"Wang","first_name":"Shuwei","full_name":"Wang, Shuwei"},{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"first_name":"Shao-Shuai","last_name":"Wang","full_name":"Wang, Shao-Shuai"},{"full_name":"Wang, Yi","last_name":"Wang","first_name":"Yi"},{"full_name":"Xuan, Wei","last_name":"Xuan","first_name":"Wei"},{"last_name":"Li","first_name":"Zhen","full_name":"Li, Zhen"},{"full_name":"Guo, Yan","last_name":"Guo","first_name":"Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"date_updated":"2023-10-04T08:23:20Z","citation":{"mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>.","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6."},"day":"05","volume":57,"article_type":"original","month":"12","date_published":"2022-12-05T00:00:00Z","date_created":"2023-01-12T11:57:00Z"},{"pmid":1,"oa_version":"Published Version","doi":"10.1083/jcb.202203139","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","type":"journal_article","year":"2022","isi":1,"article_processing_charge":"No","acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"file_date_updated":"2023-01-23T10:30:11Z","abstract":[{"text":"Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.","lang":"eng"}],"department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["36260289"],"isi":["000932958800001"]},"publication_status":"published","ddc":["580"],"_id":"12121","language":[{"iso":"eng"}],"month":"12","date_published":"2022-12-01T00:00:00Z","date_created":"2023-01-12T11:57:10Z","article_type":"original","volume":221,"has_accepted_license":"1","date_updated":"2023-08-03T14:20:15Z","file":[{"success":1,"file_name":"2022_JCB_Zhao.pdf","date_updated":"2023-01-23T10:30:11Z","checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","date_created":"2023-01-23T10:30:11Z","creator":"dernst","relation":"main_file","file_id":"12342","file_size":10365777,"access_level":"open_access","content_type":"application/pdf"}],"day":"01","citation":{"ista":"Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139.","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>","mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>.","chicago":"Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>.","apa":"Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>","short":"J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022).","ieee":"J. Zhao <i>et al.</i>, “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022."},"author":[{"first_name":"Jierui","last_name":"Zhao","full_name":"Zhao, Jierui"},{"first_name":"Mai Thu","last_name":"Bui","full_name":"Bui, Mai Thu"},{"full_name":"Ma, Juncai","first_name":"Juncai","last_name":"Ma"},{"last_name":"Künzl","first_name":"Fabian","full_name":"Künzl, Fabian"},{"first_name":"Lorenzo","last_name":"Picchianti","full_name":"Picchianti, Lorenzo"},{"last_name":"De La Concepcion","first_name":"Juan Carlos","full_name":"De La Concepcion, Juan Carlos"},{"full_name":"Chen, Yixuan","first_name":"Yixuan","last_name":"Chen"},{"full_name":"Petsangouraki, Sofia","last_name":"Petsangouraki","first_name":"Sofia"},{"last_name":"Mohseni","first_name":"Azadeh","full_name":"Mohseni, Azadeh"},{"last_name":"García-Leon","first_name":"Marta","full_name":"García-Leon, Marta"},{"first_name":"Marta Salas","last_name":"Gomez","full_name":"Gomez, Marta Salas"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","first_name":"Caterina","last_name":"Giannini"},{"first_name":"Dubois","last_name":"Gwennogan","full_name":"Gwennogan, Dubois"},{"full_name":"Kobylinska, Roksolana","first_name":"Roksolana","last_name":"Kobylinska"},{"first_name":"Marion","last_name":"Clavel","full_name":"Clavel, Marion"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Byung-Ho","last_name":"Kang","full_name":"Kang, Byung-Ho"},{"full_name":"Dagdas, Yasin","first_name":"Yasin","last_name":"Dagdas"}],"oa":1,"status":"public","article_number":"e202203139","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","intvolume":"       221","publication":"Journal of Cell Biology","publisher":"Rockefeller University Press","keyword":["Cell Biology"],"quality_controlled":"1","issue":"12"},{"oa_version":"Published Version","pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"doi":"10.1083/jcb.202107134","scopus_import":"1","isi":1,"type":"journal_article","year":"2022","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"file_date_updated":"2023-08-16T11:24:53Z","article_processing_charge":"No","acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","abstract":[{"text":"Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.","lang":"eng"}],"external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"project":[{"name":"Tools for automation and feedback microscopy","grant_number":"CZI01","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"ddc":["570"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"12122","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2022-12-05T00:00:00Z","date_created":"2023-01-12T12:01:09Z","month":"12","has_accepted_license":"1","volume":221,"article_type":"original","file":[{"file_name":"2023_JCB_Weier.pdf","success":1,"date_updated":"2023-08-16T11:24:53Z","checksum":"0c9af38f82af30c6ce528f2caece4246","date_created":"2023-08-16T11:24:53Z","relation":"main_file","creator":"dernst","file_id":"14065","file_size":11090179,"access_level":"open_access","content_type":"application/pdf"}],"day":"05","citation":{"chicago":"Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>.","ista":"Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134.","ama":"Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>","mla":"Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>.","short":"A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022).","apa":"Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>","ieee":"A.-K. Weier <i>et al.</i>, “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022."},"date_updated":"2023-08-16T11:29:12Z","oa":1,"author":[{"full_name":"Weier, Ann-Kathrin","first_name":"Ann-Kathrin","last_name":"Weier"},{"full_name":"Homrich, Mirka","last_name":"Homrich","first_name":"Mirka"},{"full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie","last_name":"Ebbinghaus"},{"full_name":"Juda, Pavel","first_name":"Pavel","last_name":"Juda"},{"full_name":"Miková, Eliška","last_name":"Miková","first_name":"Eliška"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"last_name":"Zhang","first_name":"Lili","full_name":"Zhang, Lili"},{"last_name":"Quast","first_name":"Thomas","full_name":"Quast, Thomas"},{"first_name":"Elvira","last_name":"Mass","full_name":"Mass, Elvira"},{"last_name":"Schlitzer","first_name":"Andreas","full_name":"Schlitzer, Andreas"},{"last_name":"Kolanus","first_name":"Waldemar","full_name":"Kolanus, Waldemar"},{"full_name":"Burgdorf, Sven","last_name":"Burgdorf","first_name":"Sven"},{"first_name":"Oliver J.","last_name":"Gruß","full_name":"Gruß, Oliver J."},{"first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav"},{"full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser"},{"full_name":"Kiermaier, Eva","last_name":"Kiermaier","first_name":"Eva"}],"article_number":"e202107134","title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","status":"public","publisher":"Rockefeller University Press","quality_controlled":"1","keyword":["Cell Biology"],"intvolume":"       221","publication":"Journal of Cell Biology","issue":"12"},{"department":[{"_id":"BiCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000886534000001"]},"_id":"12128","language":[{"iso":"eng"}],"publication_status":"published","ddc":["000"],"acknowledgement":"C P acknowledges funding from Astex through the Sustaining Innovation Program under the Milner Consortium. B C acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant EP/P020259/1. F A F acknowledges funding from the Swiss National Science Foundation (Grant No. P2BSP2_191736). ","article_processing_charge":"No","file_date_updated":"2023-01-23T10:42:04Z","publication_identifier":{"issn":["2632-2153"]},"abstract":[{"text":"We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.","lang":"eng"}],"isi":1,"type":"journal_article","year":"2022","scopus_import":"1","oa_version":"Published Version","doi":"10.1088/2632-2153/ac4d11","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Machine Learning: Science and Technology","intvolume":"         3","quality_controlled":"1","keyword":["Artificial Intelligence","Human-Computer Interaction","Software"],"publisher":"IOP Publishing","issue":"4","author":[{"last_name":"Poelking","first_name":"Carl","full_name":"Poelking, Carl"},{"full_name":"Faber, Felix A","first_name":"Felix A","last_name":"Faber"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing"}],"oa":1,"status":"public","title":"BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale","article_number":"040501","date_updated":"2023-08-04T08:49:53Z","day":"17","citation":{"ieee":"C. Poelking, F. A. Faber, and B. Cheng, “BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale,” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4. IOP Publishing, 2022.","apa":"Poelking, C., Faber, F. A., &#38; Cheng, B. (2022). BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>","short":"C. Poelking, F.A. Faber, B. Cheng, Machine Learning: Science and Technology 3 (2022).","chicago":"Poelking, Carl, Felix A Faber, and Bingqing Cheng. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>.","mla":"Poelking, Carl, et al. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4, 040501, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>.","ama":"Poelking C, Faber FA, Cheng B. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>","ista":"Poelking C, Faber FA, Cheng B. 2022. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. 3(4), 040501."},"file":[{"date_updated":"2023-01-23T10:42:04Z","success":1,"file_name":"2022_MachLearning_Poelking.pdf","checksum":"8930d4ad6ed9b47358c6f1a68666adb6","file_size":13814559,"creator":"dernst","file_id":"12343","relation":"main_file","date_created":"2023-01-23T10:42:04Z","content_type":"application/pdf","access_level":"open_access"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/capoe/benchml"}]},"month":"11","date_published":"2022-11-17T00:00:00Z","date_created":"2023-01-12T12:02:21Z","volume":3,"article_type":"original","has_accepted_license":"1"},{"scopus_import":"1","isi":1,"year":"2022","type":"journal_article","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00454-022-00436-2","oa_version":"Published Version","ddc":["510"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"12129","external_id":{"isi":["000883222200003"]},"department":[{"_id":"UlWa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations.","lang":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"file_date_updated":"2023-01-23T11:10:03Z","acknowledgement":"This is a full and revised version of [38] (on partial triangulations) in Proceedings of the 36th Annual International Symposium on Computational Geometry (SoCG‘20) and of some of the results in [37] (on full triangulations) in Proceedings of the 31st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA‘20).\r\nThis research started at the 11th Gremo’s Workshop on Open Problems (GWOP), Alp Sellamatt, Switzerland, June 24–28, 2013, motivated by a question posed by Filip Mori´c on full triangulations. Research was supported by the Swiss National Science Foundation within the collaborative DACH project Arrangements and Drawings as SNSF Project 200021E-171681, and by IST Austria and Berlin Free University during a sabbatical stay of the second author. We thank Michael Joswig, Jesús De Loera, and Francisco Santos for helpful discussions on the topics of this paper, and Daniel Bertschinger and Valentin Stoppiello for carefully reading earlier versions and for many helpful comments.\r\nOpen access funding provided by the Swiss Federal Institute of Technology Zürich","article_processing_charge":"No","related_material":{"record":[{"relation":"earlier_version","id":"7807","status":"public"},{"relation":"earlier_version","id":"7990","status":"public"}]},"file":[{"checksum":"307e879d09e52eddf5b225d0aaa9213a","file_name":"2022_DiscreteCompGeometry_Wagner.pdf","success":1,"date_updated":"2023-01-23T11:10:03Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-23T11:10:03Z","file_size":1747581,"relation":"main_file","file_id":"12345","creator":"dernst"}],"day":"14","citation":{"apa":"Wagner, U., &#38; Welzl, E. (2022). Connectivity of triangulation flip graphs in the plane. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00436-2\">https://doi.org/10.1007/s00454-022-00436-2</a>","short":"U. Wagner, E. Welzl, Discrete &#38; Computational Geometry 68 (2022) 1227–1284.","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane,” <i>Discrete &#38; Computational Geometry</i>, vol. 68, no. 4. Springer Nature, pp. 1227–1284, 2022.","ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane. <i>Discrete &#38; Computational Geometry</i>. 2022;68(4):1227-1284. doi:<a href=\"https://doi.org/10.1007/s00454-022-00436-2\">10.1007/s00454-022-00436-2</a>","ista":"Wagner U, Welzl E. 2022. Connectivity of triangulation flip graphs in the plane. Discrete &#38; Computational Geometry. 68(4), 1227–1284.","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” <i>Discrete &#38; Computational Geometry</i>, vol. 68, no. 4, Springer Nature, 2022, pp. 1227–84, doi:<a href=\"https://doi.org/10.1007/s00454-022-00436-2\">10.1007/s00454-022-00436-2</a>.","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00436-2\">https://doi.org/10.1007/s00454-022-00436-2</a>."},"date_updated":"2023-08-04T08:51:08Z","has_accepted_license":"1","article_type":"original","volume":68,"date_published":"2022-11-14T00:00:00Z","date_created":"2023-01-12T12:02:28Z","month":"11","issue":"4","publisher":"Springer Nature","quality_controlled":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"page":"1227-1284","intvolume":"        68","publication":"Discrete & Computational Geometry","title":"Connectivity of triangulation flip graphs in the plane","status":"public","oa":1,"author":[{"first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"},{"full_name":"Welzl, Emo","first_name":"Emo","last_name":"Welzl"}]},{"quality_controlled":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publisher":"Springer Nature","publication":"Nature Communications","intvolume":"        13","oa":1,"author":[{"full_name":"Huang, Jian","last_name":"Huang","first_name":"Jian"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"full_name":"Malik, Shikha","last_name":"Malik","first_name":"Shikha"},{"full_name":"Gentile, Benjamin R.","last_name":"Gentile","first_name":"Benjamin R."},{"full_name":"Xiong, Va","first_name":"Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","first_name":"Tzahi","last_name":"Arazi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Zhao, Dazhong","first_name":"Dazhong","last_name":"Zhao"}],"title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","article_number":"6960","status":"public","day":"15","citation":{"chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>.","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022)."},"file":[{"file_size":3375249,"creator":"dernst","file_id":"12346","relation":"main_file","date_created":"2023-01-23T11:17:33Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-23T11:17:33Z","file_name":"2022_NatureCommunications_Huang.pdf","success":1,"checksum":"233922a7b9507d9d48591e6799e4526e"}],"date_updated":"2023-08-04T08:52:01Z","date_created":"2023-01-12T12:02:41Z","date_published":"2022-11-15T00:00:00Z","month":"11","has_accepted_license":"1","volume":13,"article_type":"original","external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12130","language":[{"iso":"eng"}],"publication_status":"published","ddc":["580"],"file_date_updated":"2023-01-23T11:17:33Z","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","abstract":[{"lang":"eng","text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants."}],"isi":1,"type":"journal_article","year":"2022","scopus_import":"1","oa_version":"Published Version","pmid":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-022-34723-6"},{"has_accepted_license":"1","article_type":"original","volume":7,"date_published":"2022-11-15T00:00:00Z","date_created":"2023-01-12T12:02:54Z","month":"11","day":"15","citation":{"ieee":"M. G. Byazrova <i>et al.</i>, “Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination,” <i>npj Vaccines</i>, vol. 7. Springer Nature, 2022.","short":"M.G. Byazrova, E.A. Astakhova, A. Minnegalieva, M.M. Sukhova, A.A. Mikhailov, A.G. Prilipov, A.A. Gorchakov, A.V. Filatov, Npj Vaccines 7 (2022).","apa":"Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G., … Filatov, A. V. (2022). Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. <i>Npj Vaccines</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41541-022-00566-x\">https://doi.org/10.1038/s41541-022-00566-x</a>","chicago":"Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M. Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” <i>Npj Vaccines</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41541-022-00566-x\">https://doi.org/10.1038/s41541-022-00566-x</a>.","mla":"Byazrova, Maria G., et al. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” <i>Npj Vaccines</i>, vol. 7, 145, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41541-022-00566-x\">10.1038/s41541-022-00566-x</a>.","ama":"Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. <i>npj Vaccines</i>. 2022;7. doi:<a href=\"https://doi.org/10.1038/s41541-022-00566-x\">10.1038/s41541-022-00566-x</a>","ista":"Byazrova MG, Astakhova EA, Minnegalieva A, Sukhova MM, Mikhailov AA, Prilipov AG, Gorchakov AA, Filatov AV. 2022. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 7, 145."},"file":[{"file_size":1856046,"relation":"main_file","file_id":"12347","creator":"dernst","date_created":"2023-01-23T11:22:09Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-23T11:22:09Z","success":1,"file_name":"2022_njpVaccines_Byazrova.pdf","checksum":"ddaac096381565b2b4b7dcc34cdbc4ee"}],"date_updated":"2023-08-04T08:52:40Z","title":"Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination","article_number":"145","status":"public","oa":1,"author":[{"last_name":"Byazrova","first_name":"Maria G.","full_name":"Byazrova, Maria G."},{"full_name":"Astakhova, Ekaterina A.","last_name":"Astakhova","first_name":"Ekaterina A."},{"full_name":"Minnegalieva, Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","first_name":"Aygul","last_name":"Minnegalieva"},{"last_name":"Sukhova","first_name":"Maria M.","full_name":"Sukhova, Maria M."},{"first_name":"Artem A.","last_name":"Mikhailov","full_name":"Mikhailov, Artem A."},{"full_name":"Prilipov, Alexey G.","last_name":"Prilipov","first_name":"Alexey G."},{"last_name":"Gorchakov","first_name":"Andrey A.","full_name":"Gorchakov, Andrey A."},{"full_name":"Filatov, Alexander V.","last_name":"Filatov","first_name":"Alexander V."}],"quality_controlled":"1","keyword":["Pharmacology (medical)","Infectious Diseases","Pharmacology","Immunology","SARS-COV-2","COVID"],"publisher":"Springer Nature","publication":"npj Vaccines","intvolume":"         7","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41541-022-00566-x","oa_version":"Published Version","pmid":1,"year":"2022","type":"journal_article","isi":1,"scopus_import":"1","abstract":[{"text":"Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines.","lang":"eng"}],"file_date_updated":"2023-01-23T11:22:09Z","publication_identifier":{"issn":["2059-0105"]},"acknowledgement":"We thank Sergey Kulemzin, Grigory Efimov, Yuri Lebedin, Alexander Taranin and Rudolf Valenta for providing reagents. Figures were created with the help of BioRender.com. This work was supported by the Russian Science Foundation (Project 21-15-00286). Byazrova M.G. was supported by the RUDN University Strategic Academic Leadership Program.","article_processing_charge":"No","_id":"12131","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570"],"external_id":{"pmid":["36379998"],"isi":["000884278600004"]},"department":[{"_id":"FyKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"12133","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"pmid":["36284178"],"isi":["000871836300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SyCr"},{"_id":"MiSi"}],"abstract":[{"text":"Social distancing is an effective way to prevent the spread of disease in societies, whereas infection elimination is a key element of organismal immunity. Here, we discuss how the study of social insects such as ants — which form a superorganism of unconditionally cooperative individuals and thus represent a level of organization that is intermediate between a classical society of individuals and an organism of cells — can help to determine common principles of disease defence across levels of organization.","lang":"eng"}],"publication_identifier":{"issn":["1474-1733"],"eissn":["1474-1741"]},"article_processing_charge":"No","isi":1,"year":"2022","type":"journal_article","scopus_import":"1","doi":"10.1038/s41577-022-00797-y","oa_version":"None","pmid":1,"issue":"12","page":"713-714","keyword":["Energy Engineering and Power Technology","Fuel Technology"],"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Reviews Immunology","intvolume":"        22","title":"Principles of disease defence in organisms, superorganisms and societies","status":"public","author":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"day":"01","citation":{"short":"S. Cremer, M.K. Sixt, Nature Reviews Immunology 22 (2022) 713–714.","apa":"Cremer, S., &#38; Sixt, M. K. (2022). Principles of disease defence in organisms, superorganisms and societies. <i>Nature Reviews Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41577-022-00797-y\">https://doi.org/10.1038/s41577-022-00797-y</a>","ieee":"S. Cremer and M. K. Sixt, “Principles of disease defence in organisms, superorganisms and societies,” <i>Nature Reviews Immunology</i>, vol. 22, no. 12. Springer Nature, pp. 713–714, 2022.","ama":"Cremer S, Sixt MK. Principles of disease defence in organisms, superorganisms and societies. <i>Nature Reviews Immunology</i>. 2022;22(12):713-714. doi:<a href=\"https://doi.org/10.1038/s41577-022-00797-y\">10.1038/s41577-022-00797-y</a>","ista":"Cremer S, Sixt MK. 2022. Principles of disease defence in organisms, superorganisms and societies. Nature Reviews Immunology. 22(12), 713–714.","mla":"Cremer, Sylvia, and Michael K. Sixt. “Principles of Disease Defence in Organisms, Superorganisms and Societies.” <i>Nature Reviews Immunology</i>, vol. 22, no. 12, Springer Nature, 2022, pp. 713–14, doi:<a href=\"https://doi.org/10.1038/s41577-022-00797-y\">10.1038/s41577-022-00797-y</a>.","chicago":"Cremer, Sylvia, and Michael K Sixt. “Principles of Disease Defence in Organisms, Superorganisms and Societies.” <i>Nature Reviews Immunology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41577-022-00797-y\">https://doi.org/10.1038/s41577-022-00797-y</a>."},"date_updated":"2023-08-04T08:53:32Z","article_type":"letter_note","volume":22,"date_published":"2022-12-01T00:00:00Z","date_created":"2023-01-12T12:03:14Z","month":"12"},{"scopus_import":"1","type":"journal_article","year":"2022","doi":"10.1088/2632-072x/ac99cd","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","ddc":["530"],"_id":"12134","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the type of phase transition. In particular, we uncover three distinct types of explosive phase transitions for epidemic dynamics with capacity-limited interventions. Depending on the capacity limit, interventions may (i) leave the standard second order phase transition unchanged but exponentially suppress the probability of large outbreaks, (ii) induce a first-order discontinuous transition to macroscopic outbreaks, or (iii) cause a secondary explosive yet continuous third-order transition. These insights highlight inherent limitations in predicting and containing epidemic outbreaks. More generally our study offers a cornerstone example of a third-order explosive phase transition in complex systems."}],"article_processing_charge":"No","acknowledgement":"We acknowledge support from the Volkswagen Foundation under Grant No. 99720 and the German Federal Ministry for Education and Research (BMBF) under Grant No. 16ICR01. This research was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2068—390729961—Cluster of Excellence Physics of Life of TU Dresden.","publication_identifier":{"issn":["2632-072X"]},"file_date_updated":"2023-01-24T07:24:37Z","date_updated":"2023-02-13T09:15:13Z","file":[{"checksum":"35c5c5cb0eb17ea1b5184755daab9fc9","date_updated":"2023-01-24T07:24:37Z","file_name":"2022_JourPhysics_Boerner.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12350","creator":"dernst","file_size":1006106,"date_created":"2023-01-24T07:24:37Z"}],"citation":{"ieee":"G. Börner, M. Schröder, D. Scarselli, N. B. Budanur, B. Hof, and M. Timme, “Explosive transitions in epidemic dynamics,” <i>Journal of Physics: Complexity</i>, vol. 3, no. 4. IOP Publishing, 2022.","apa":"Börner, G., Schröder, M., Scarselli, D., Budanur, N. B., Hof, B., &#38; Timme, M. (2022). Explosive transitions in epidemic dynamics. <i>Journal of Physics: Complexity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">https://doi.org/10.1088/2632-072x/ac99cd</a>","short":"G. Börner, M. Schröder, D. Scarselli, N.B. Budanur, B. Hof, M. Timme, Journal of Physics: Complexity 3 (2022).","mla":"Börner, Georg, et al. “Explosive Transitions in Epidemic Dynamics.” <i>Journal of Physics: Complexity</i>, vol. 3, no. 4, 04LT02, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">10.1088/2632-072x/ac99cd</a>.","ista":"Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. 2022. Explosive transitions in epidemic dynamics. Journal of Physics: Complexity. 3(4), 04LT02.","ama":"Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. Explosive transitions in epidemic dynamics. <i>Journal of Physics: Complexity</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">10.1088/2632-072x/ac99cd</a>","chicago":"Börner, Georg, Malte Schröder, Davide Scarselli, Nazmi B Budanur, Björn Hof, and Marc Timme. “Explosive Transitions in Epidemic Dynamics.” <i>Journal of Physics: Complexity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">https://doi.org/10.1088/2632-072x/ac99cd</a>."},"day":"25","volume":3,"article_type":"original","has_accepted_license":"1","month":"10","date_created":"2023-01-12T12:03:43Z","date_published":"2022-10-25T00:00:00Z","issue":"4","intvolume":"         3","publication":"Journal of Physics: Complexity","publisher":"IOP Publishing","keyword":["Artificial Intelligence","Computer Networks and Communications","Computer Science Applications","Information Systems"],"quality_controlled":"1","status":"public","article_number":"04LT02","title":"Explosive transitions in epidemic dynamics","author":[{"full_name":"Börner, Georg","first_name":"Georg","last_name":"Börner"},{"full_name":"Schröder, Malte","last_name":"Schröder","first_name":"Malte"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","last_name":"Scarselli","orcid":"0000-0001-5227-4271","first_name":"Davide"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"},{"last_name":"Timme","first_name":"Marc","full_name":"Timme, Marc"}],"oa":1},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1145/3550469.3555406","oa_version":"Published Version","scopus_import":"1","type":"conference","year":"2022","abstract":[{"lang":"eng","text":"A good match of material appearance between real-world objects and their digital on-screen representations is critical for many applications such as fabrication, design, and e-commerce. However, faithful appearance reproduction is challenging, especially for complex phenomena, such as gloss. In most cases, the view-dependent nature of gloss and the range of luminance values required for reproducing glossy materials exceeds the current capabilities of display devices. As a result, appearance reproduction poses significant problems even with accurately rendered images. This paper studies the gap between the gloss perceived from real-world objects and their digital counterparts. Based on our psychophysical experiments on a wide range of 3D printed samples and their corresponding photographs, we derive insights on the influence of geometry, illumination, and the display’s brightness and measure the change in gloss appearance due to the display limitations. Our evaluation experiments demonstrate that using the prediction to correct material parameters in a rendering system improves the match of gloss appearance between real objects and their visualization on a display device."}],"publication_identifier":{"isbn":["9781450394703"]},"file_date_updated":"2023-01-24T07:35:21Z","article_processing_charge":"No","acknowledgement":"This work is supported by FWF Lise Meitner (Grant M 3319), European Research Council (project CHAMELEON, Grant no. 682080), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta.","publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"_id":"12135","project":[{"name":"Perception-Aware Appearance Fabrication","grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeBi"}],"has_accepted_license":"1","volume":2022,"date_published":"2022-11-01T00:00:00Z","date_created":"2023-01-12T12:03:56Z","month":"11","conference":{"end_date":"2022-12-09","location":"Daegu, South Korea","start_date":"2022-12-06","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":28826826,"creator":"dernst","relation":"main_file","file_id":"12351","date_created":"2023-01-24T07:35:21Z","checksum":"f47f3215ab8bb919e3546b3438c34c21","date_updated":"2023-01-24T07:35:21Z","file_name":"2022_ACM_SIGGRAPH_Chen.pdf","success":1}],"citation":{"mla":"Chen, Bin, et al. “Gloss Management for Consistent Reproduction of Real and Virtual Objects.” <i>SIGGRAPH Asia 2022 Conference Papers</i>, vol. 2022, 35, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3550469.3555406\">10.1145/3550469.3555406</a>.","ista":"Chen B, Piovarci M, Wang C, Seidel H-P, Didyk P, Myszkowski K, Serrano A. 2022. Gloss management for consistent reproduction of real and virtual objects. SIGGRAPH Asia 2022 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference vol. 2022, 35.","ama":"Chen B, Piovarci M, Wang C, et al. Gloss management for consistent reproduction of real and virtual objects. In: <i>SIGGRAPH Asia 2022 Conference Papers</i>. Vol 2022. Association for Computing Machinery; 2022. doi:<a href=\"https://doi.org/10.1145/3550469.3555406\">10.1145/3550469.3555406</a>","chicago":"Chen, Bin, Michael Piovarci, Chao Wang, Hans-Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “Gloss Management for Consistent Reproduction of Real and Virtual Objects.” In <i>SIGGRAPH Asia 2022 Conference Papers</i>, Vol. 2022. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3550469.3555406\">https://doi.org/10.1145/3550469.3555406</a>.","ieee":"B. Chen <i>et al.</i>, “Gloss management for consistent reproduction of real and virtual objects,” in <i>SIGGRAPH Asia 2022 Conference Papers</i>, Daegu, South Korea, 2022, vol. 2022.","short":"B. Chen, M. Piovarci, C. Wang, H.-P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, in:, SIGGRAPH Asia 2022 Conference Papers, Association for Computing Machinery, 2022.","apa":"Chen, B., Piovarci, M., Wang, C., Seidel, H.-P., Didyk, P., Myszkowski, K., &#38; Serrano, A. (2022). Gloss management for consistent reproduction of real and virtual objects. In <i>SIGGRAPH Asia 2022 Conference Papers</i> (Vol. 2022). Daegu, South Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3550469.3555406\">https://doi.org/10.1145/3550469.3555406</a>"},"day":"01","date_updated":"2023-02-13T09:15:25Z","article_number":"35","title":"Gloss management for consistent reproduction of real and virtual objects","status":"public","oa":1,"author":[{"full_name":"Chen, Bin","last_name":"Chen","first_name":"Bin"},{"full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci","first_name":"Michael"},{"last_name":"Wang","first_name":"Chao","full_name":"Wang, Chao"},{"full_name":"Seidel, Hans-Peter","last_name":"Seidel","first_name":"Hans-Peter"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"},{"full_name":"Serrano, Ana","last_name":"Serrano","first_name":"Ana"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","intvolume":"      2022","publication":"SIGGRAPH Asia 2022 Conference Papers"},{"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2207.12990","open_access":"1"}],"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","Applied Mathematics"],"quality_controlled":"1","publisher":"Cambridge University Press","publication":"Journal of Fluid Mechanics","intvolume":"       951","title":"Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow","article_number":"A21","status":"public","oa":1,"author":[{"first_name":"B.","last_name":"Wang","full_name":"Wang, B."},{"full_name":"Ayats López, Roger","id":"ab77522d-073b-11ed-8aff-e71b39258362","first_name":"Roger","orcid":"0000-0001-6572-0621","last_name":"Ayats López"},{"full_name":"Deguchi, K.","first_name":"K.","last_name":"Deguchi"},{"full_name":"Mellibovsky, F.","first_name":"F.","last_name":"Mellibovsky"},{"last_name":"Meseguer","first_name":"A.","full_name":"Meseguer, A."}],"citation":{"apa":"Wang, B., Ayats López, R., Deguchi, K., Mellibovsky, F., &#38; Meseguer, A. (2022). Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.828\">https://doi.org/10.1017/jfm.2022.828</a>","short":"B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, A. Meseguer, Journal of Fluid Mechanics 951 (2022).","ieee":"B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer, “Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow,” <i>Journal of Fluid Mechanics</i>, vol. 951. Cambridge University Press, 2022.","chicago":"Wang, B., Roger Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer. “Self-Sustainment of Coherent Structures in Counter-Rotating Taylor–Couette Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/jfm.2022.828\">https://doi.org/10.1017/jfm.2022.828</a>.","ista":"Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. 2022. Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. Journal of Fluid Mechanics. 951, A21.","ama":"Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. <i>Journal of Fluid Mechanics</i>. 2022;951. doi:<a href=\"https://doi.org/10.1017/jfm.2022.828\">10.1017/jfm.2022.828</a>","mla":"Wang, B., et al. “Self-Sustainment of Coherent Structures in Counter-Rotating Taylor–Couette Flow.” <i>Journal of Fluid Mechanics</i>, vol. 951, A21, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/jfm.2022.828\">10.1017/jfm.2022.828</a>."},"day":"07","date_updated":"2023-08-04T08:54:16Z","volume":951,"article_type":"original","date_published":"2022-11-07T00:00:00Z","date_created":"2023-01-12T12:04:17Z","month":"11","_id":"12137","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000879446900001"],"arxiv":["2207.12990"]},"department":[{"_id":"BjHo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We investigate the local self-sustained process underlying spiral turbulence in counter-rotating Taylor–Couette flow using a periodic annular domain, shaped as a parallelogram, two of whose sides are aligned with the cylindrical helix described by the spiral pattern. The primary focus of the study is placed on the emergence of drifting–rotating waves (DRW) that capture, in a relatively small domain, the main features of coherent structures typically observed in developed turbulence. The transitional dynamics of the subcritical region, far below the first instability of the laminar circular Couette flow, is determined by the upper and lower branches of DRW solutions originated at saddle-node bifurcations. The mechanism whereby these solutions self-sustain, and the chaotic dynamics they induce, are conspicuously reminiscent of other subcritical shear flows. Remarkably, the flow properties of DRW persist even as the Reynolds number is increased beyond the linear stability threshold of the base flow. Simulations in a narrow parallelogram domain stretched in the azimuthal direction to revolve around the apparatus a full turn confirm that self-sustained vortices eventually concentrate into a localised pattern. The resulting statistical steady state satisfactorily reproduces qualitatively, and to a certain degree also quantitatively, the topology and properties of spiral turbulence as calculated in a large periodic domain of sufficient aspect ratio that is representative of the real system.","lang":"eng"}],"publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"acknowledgement":"K.D.’s research was supported by an Australian Research Council Discovery Early Career\r\nResearcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitivdad (grant numbers FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant number PID2020-114043GB-I00) and the Generalitat de Catalunya (grant 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152).","article_processing_charge":"No","type":"journal_article","isi":1,"year":"2022","arxiv":1,"scopus_import":"1","doi":"10.1017/jfm.2022.828","oa_version":"Preprint"},{"ec_funded":1,"abstract":[{"lang":"eng","text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes."}],"article_processing_charge":"No","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","file_date_updated":"2023-05-30T17:07:05Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"12138","language":[{"iso":"eng"}],"ddc":["572"],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LeSa"}],"project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"external_id":{"pmid":["36104567"],"isi":["000854788200001"]},"doi":"10.1038/s41586-022-05199-7","pmid":1,"oa_version":"Submitted Version","year":"2022","type":"journal_article","isi":1,"scopus_import":"1","status":"public","title":"A universal coupling mechanism of respiratory complex I","author":[{"last_name":"Kravchuk","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","last_name":"Petrova","full_name":"Petrova, Olga","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E"},{"last_name":"Kampjut","first_name":"Domen","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Wojciechowska-Bason","full_name":"Wojciechowska-Bason, Anna"},{"first_name":"Zara","last_name":"Breese","full_name":"Breese, Zara"},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"issue":"7928","publication":"Nature","intvolume":"       609","page":"808-814","quality_controlled":"1","keyword":["Multidisciplinary"],"publisher":"Springer Nature","article_type":"original","volume":609,"has_accepted_license":"1","month":"09","date_created":"2023-01-12T12:04:33Z","date_published":"2022-09-22T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"12781","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41586-022-05457-8","relation":"erratum"},{"relation":"press_release","url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","description":"News on ISTA website"}]},"date_updated":"2023-08-04T08:54:52Z","day":"22","citation":{"apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>","short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>.","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>."},"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2023-05-30T17:05:31Z","file_size":1425655,"creator":"lsazanov","relation":"main_file","file_id":"13104","checksum":"d42a93e24f59e883ef0b5429832391d0","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","success":1,"date_updated":"2023-05-30T17:05:31Z"},{"access_level":"open_access","content_type":"application/pdf","date_created":"2023-05-30T17:07:05Z","relation":"main_file","creator":"lsazanov","file_id":"13105","file_size":9842513,"checksum":"5422bc0a73b3daadafa262c7ea6deae3","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","success":1,"date_updated":"2023-05-30T17:07:05Z"}]},{"title":"Anomalous Shiba states in topological iron-based superconductors","article_number":"L201107","status":"public","oa":1,"author":[{"orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kirmani, Ammar","first_name":"Ammar","last_name":"Kirmani"},{"full_name":"Fernandes, Rafael M.","last_name":"Fernandes","first_name":"Rafael M."},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"issue":"20","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2207.12425","open_access":"1"}],"publisher":"American Physical Society","publication":"Physical Review B","intvolume":"       106","volume":106,"article_type":"original","date_published":"2022-11-15T00:00:00Z","date_created":"2023-01-12T12:04:43Z","month":"11","day":"15","citation":{"mla":"Ghazaryan, Areg, et al. “Anomalous Shiba States in Topological Iron-Based Superconductors.” <i>Physical Review B</i>, vol. 106, no. 20, L201107, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.106.l201107\">10.1103/physrevb.106.l201107</a>.","ista":"Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. 2022. Anomalous Shiba states in topological iron-based superconductors. Physical Review B. 106(20), L201107.","ama":"Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. Anomalous Shiba states in topological iron-based superconductors. <i>Physical Review B</i>. 2022;106(20). doi:<a href=\"https://doi.org/10.1103/physrevb.106.l201107\">10.1103/physrevb.106.l201107</a>","chicago":"Ghazaryan, Areg, Ammar Kirmani, Rafael M. Fernandes, and Pouyan Ghaemi. “Anomalous Shiba States in Topological Iron-Based Superconductors.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.106.l201107\">https://doi.org/10.1103/physrevb.106.l201107</a>.","ieee":"A. Ghazaryan, A. Kirmani, R. M. Fernandes, and P. Ghaemi, “Anomalous Shiba states in topological iron-based superconductors,” <i>Physical Review B</i>, vol. 106, no. 20. American Physical Society, 2022.","short":"A. Ghazaryan, A. Kirmani, R.M. Fernandes, P. Ghaemi, Physical Review B 106 (2022).","apa":"Ghazaryan, A., Kirmani, A., Fernandes, R. M., &#38; Ghaemi, P. (2022). Anomalous Shiba states in topological iron-based superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.106.l201107\">https://doi.org/10.1103/physrevb.106.l201107</a>"},"date_updated":"2023-08-04T08:55:31Z","abstract":[{"text":"We demonstrate the formation of robust zero-energy modes close to magnetic impurities in the iron-based superconductor FeSe1-z Tez. We find that the Zeeman field generated by the impurity favors a spin-triplet interorbital pairing as opposed to the spin-singlet intraorbital pairing prevalent in the bulk. The preferred spin-triplet pairing preserves time-reversal symmetry and is topological, as robust, topologically protected zero modes emerge at the boundary between regions with different pairing states. Moreover, the zero modes form Kramers doublets that are insensitive to the direction of the spin polarization or to the separation between impurities. We argue that our theoretical results are consistent with recent experimental measurements on FeSe1-z Tez.","lang":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_processing_charge":"No","acknowledgement":"We thank Armin Rahmani, Andrey V. Chubukov, Jay D. Sau and Ruixing Zhang for fruitful discussions. AK and PG are supported by NSF-DMR2037996. PG also acknowledges support from NSF-DMR1824265. RMF was supported by the U. S. Department of Energy, Office\r\nof Science, Basic Energy Sciences, Materials Sciences and Engineering Division, under Award No. DE-SC0020045. Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation grant PHY-1607611. ","language":[{"iso":"eng"}],"_id":"12139","publication_status":"published","external_id":{"arxiv":["2207.12425"],"isi":["000893171800001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"doi":"10.1103/physrevb.106.l201107","oa_version":"Preprint","year":"2022","arxiv":1,"type":"journal_article","isi":1,"scopus_import":"1"}]