[{"file_date_updated":"2021-06-09T15:21:14Z","department":[{"_id":"FlSc"}],"ddc":["570"],"date_updated":"2023-08-08T13:53:53Z","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9431","issue":"1","volume":12,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","relation":"press_release","description":"News on IST Homepage"}]},"file":[{"date_created":"2021-06-09T15:21:14Z","file_name":"2021_NatureCommunications_Obr.pdf","date_updated":"2021-06-09T15:21:14Z","file_size":6166295,"creator":"kschuh","file_id":"9538","checksum":"53ccc53d09a9111143839dbe7784e663","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","month":"05","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","author":[{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"first_name":"Nadia","last_name":"Nikulin","full_name":"Nikulin, Nadia"},{"full_name":"Feathers, Jon-Philip R.","last_name":"Feathers","first_name":"Jon-Philip R."},{"last_name":"Klanschnig","full_name":"Klanschnig, Marco","first_name":"Marco"},{"last_name":"Thader","full_name":"Thader, Andreas","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc C.","full_name":"Johnson, Marc C.","last_name":"Johnson"},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."}],"article_processing_charge":"No","external_id":{"isi":["000659145000011"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021."},"project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"article_number":"3226","date_published":"2021-05-28T00:00:00Z","doi":"10.1038/s41467-021-23506-0","date_created":"2021-05-28T14:25:50Z","day":"28","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","publisher":"Nature Research","quality_controlled":"1","oa":1,"acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF)."},{"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","date_published":"2021-07-25T00:00:00Z","doi":"10.1017/jfm.2021.371","date_created":"2021-06-06T22:01:30Z","has_accepted_license":"1","isi":1,"year":"2021","day":"25","publication":"Journal of Fluid Mechanics","article_number":"A17","author":[{"first_name":"Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena","last_name":"Marensi"},{"full_name":"He, Shuisheng","last_name":"He","first_name":"Shuisheng"},{"full_name":"Willis, Ashley P.","last_name":"Willis","first_name":"Ashley P."}],"external_id":{"isi":["000653785000001"],"arxiv":["2008.13486"]},"article_processing_charge":"Yes (via OA deal)","title":"Suppression of turbulence and travelling waves in a vertical heated pipe","citation":{"chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371.","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"07","intvolume":" 919","abstract":[{"text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation.","lang":"eng"}],"oa_version":"Published Version","volume":919,"publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9766","checksum":"867ad077e45c181c2c5ec1311ba27c41","success":1,"creator":"kschuh","date_updated":"2021-08-03T09:53:28Z","file_size":4087358,"date_created":"2021-08-03T09:53:28Z","file_name":"2021_JournalFluidMechanics_Marensi.pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9467","file_date_updated":"2021-08-03T09:53:28Z","department":[{"_id":"BjHo"}],"date_updated":"2023-08-08T13:58:41Z","ddc":["530"]},{"department":[{"_id":"NiBa"}],"file_date_updated":"2021-06-11T15:34:53Z","ddc":["570"],"date_updated":"2023-08-08T13:59:18Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","_id":"9470","ec_funded":1,"volume":30,"issue":"12","language":[{"iso":"eng"}],"file":[{"creator":"kschuh","date_updated":"2021-06-11T15:34:53Z","file_size":1031978,"date_created":"2021-06-11T15:34:53Z","file_name":"2021_MolecularEcology_Berdan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"e6f4731365bde2614b333040a08265d8","file_id":"9545","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"intvolume":" 30","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","article_processing_charge":"No","external_id":{"isi":["000652056400001"]},"author":[{"first_name":"Emma L.","last_name":"Berdan","full_name":"Berdan, Emma L."},{"first_name":"Alexandre","last_name":"Blanckaert","full_name":"Blanckaert, Alexandre"},{"last_name":"Slotte","full_name":"Slotte, Tanja","first_name":"Tanja"},{"full_name":"Suh, Alexander","last_name":"Suh","first_name":"Alexander"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021."},"project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}],"date_created":"2021-06-06T22:01:31Z","doi":"10.1111/mec.15936","date_published":"2021-06-01T00:00:00Z","page":"2710-2723","publication":"Molecular Ecology","day":"01","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018)."},{"status":"public","article_type":"original","type":"journal_article","_id":"9468","department":[{"_id":"UlWa"}],"date_updated":"2023-08-08T13:58:12Z","month":"05","intvolume":" 35","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2001.06053","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n","lang":"eng"}],"issue":"2","volume":35,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["08954801"]},"publication_status":"published","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Extending drawings of complete graphs into arrangements of pseudocircles","author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara"},{"first_name":"R. Bruce","last_name":"Richter","full_name":"Richter, R. Bruce"},{"first_name":"Matthew","full_name":"Sunohara, Matthew","last_name":"Sunohara"}],"external_id":{"arxiv":["2001.06053"],"isi":["000674142200022"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234","apa":"Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076.","chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234."},"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"date_published":"2021-05-20T00:00:00Z","doi":"10.1137/20M1313234","date_created":"2021-06-06T22:01:30Z","page":"1050-1076","day":"20","publication":"SIAM Journal on Discrete Mathematics","isi":1,"year":"2021"},{"month":"09","intvolume":" 281","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2009.00992","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions.","lang":"eng"}],"issue":"6","volume":281,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"9462","department":[{"_id":"RoSe"}],"date_updated":"2023-08-08T13:56:27Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","doi":"10.1016/j.jfa.2021.109096","date_published":"2021-09-15T00:00:00Z","date_created":"2021-06-06T22:01:28Z","day":"15","publication":"Journal of Functional Analysis","isi":1,"year":"2021","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_number":"109096","title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","author":[{"last_name":"Deuchert","full_name":"Deuchert, Andreas","first_name":"Andreas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"external_id":{"isi":["000656508600008"],"arxiv":["2009.00992"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096"}},{"abstract":[{"lang":"eng","text":"In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis."}],"oa_version":"None","scopus_import":"1","month":"05","publication_status":"published","publication_identifier":{"eissn":["1029-4937"],"issn":["1055-6788"]},"language":[{"iso":"eng"}],"ec_funded":1,"_id":"9469","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-08T13:57:43Z","department":[{"_id":"VlKo"}],"acknowledgement":"The authors are grateful to the anonymous referees and the handling Editor for their insightful comments which have improved the earlier version of the manuscript greatly. The second author is grateful to the University of Hafr Al Batin. The last author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","publisher":"Taylor and Francis","quality_controlled":"1","year":"2021","isi":1,"publication":"Optimization Methods and Software","day":"12","date_created":"2021-06-06T22:01:30Z","date_published":"2021-05-12T00:00:00Z","doi":"10.1080/10556788.2021.1924715","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"citation":{"short":"O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).","ieee":"O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting method for monotone inclusion problem,” Optimization Methods and Software. Taylor and Francis, 2021.","apa":"Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715","ama":"Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715","mla":"Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software, Taylor and Francis, 2021, doi:10.1080/10556788.2021.1924715.","ista":"Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software.","chicago":"Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000650507600001"]},"article_processing_charge":"No","author":[{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"first_name":"Cyril D.","full_name":"Enyi, Cyril D.","last_name":"Enyi"},{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139"}],"title":"Reflected three-operator splitting method for monotone inclusion problem"},{"date_updated":"2023-08-08T14:05:26Z","ddc":["570"],"department":[{"_id":"EM-Fac"}],"file_date_updated":"2021-06-15T18:55:59Z","_id":"9540","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"creator":"cziletti","date_updated":"2021-06-15T18:55:59Z","file_size":3397292,"date_created":"2021-06-15T18:55:59Z","file_name":"2021_NatureComm_Prattes.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"40fc24c1310930990b52a8ad1142ee97","file_id":"9556","success":1}],"language":[{"iso":"eng"}],"issue":"1","volume":12,"abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"month":"06","intvolume":" 12","citation":{"mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x.","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","last_name":"Rössler","full_name":"Rössler, Ingrid"},{"first_name":"Isabella","last_name":"Klein","full_name":"Klein, Isabella"},{"first_name":"Christina","last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"first_name":"Christian C.","full_name":"Gruber, Christian C.","last_name":"Gruber"},{"first_name":"Karl","last_name":"Gruber","full_name":"Gruber, Karl"},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"first_name":"Helmut","full_name":"Bergler, Helmut","last_name":"Bergler"}],"article_processing_charge":"No","external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","article_number":"3483","has_accepted_license":"1","isi":1,"year":"2021","day":"09","publication":"Nature Communications","date_published":"2021-06-09T00:00:00Z","doi":"10.1038/s41467-021-23854-x","date_created":"2021-06-10T14:57:45Z","acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"volume":594,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"intvolume":" 594","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-021-03613-0"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. "}],"department":[{"_id":"PeJo"}],"date_updated":"2023-08-08T13:59:51Z","status":"public","article_type":"original","type":"journal_article","_id":"9549","date_created":"2021-06-13T22:01:33Z","doi":"10.1038/s41586-021-03613-0","date_published":"2021-06-02T00:00:00Z","page":"454-458","publication":"Nature","day":"02","year":"2021","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.","title":"Gating and modulation of a hetero-octameric AMPA glutamate receptor","article_processing_charge":"No","external_id":{"pmid":["34079129"],"isi":["000657238100003"]},"author":[{"last_name":"Zhang","full_name":"Zhang, Danyang","first_name":"Danyang"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson"},{"first_name":"Peter M.","full_name":"Matthews, Peter M.","last_name":"Matthews"},{"last_name":"Cais","full_name":"Cais, Ondrej","first_name":"Ondrej"},{"first_name":"Ingo H.","last_name":"Greger","full_name":"Greger, Ingo H."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.","chicago":"Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.","ieee":"D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol. 594. Springer Nature, pp. 454–458, 2021.","short":"D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458.","ama":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0","apa":"Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03613-0","mla":"Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0."}},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. "}],"intvolume":" 9","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2021_ForumMath_Bao.pdf","date_created":"2021-06-15T14:40:45Z","creator":"cziletti","file_size":483458,"date_updated":"2021-06-15T14:40:45Z","success":1,"checksum":"47c986578de132200d41e6d391905519","file_id":"9555","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["20505094"]},"ec_funded":1,"volume":9,"_id":"9550","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-08-08T14:03:40Z","file_date_updated":"2021-06-15T14:40:45Z","department":[{"_id":"LaEr"}],"acknowledgement":"The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","publication":"Forum of Mathematics, Sigma","day":"27","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-06-13T22:01:33Z","doi":"10.1017/fms.2021.38","date_published":"2021-05-27T00:00:00Z","article_number":"e44","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.","short":"Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).","ama":"Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.38","mla":"Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.","ista":"Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.38."},"title":"Equipartition principle for Wigner matrices","external_id":{"arxiv":["2008.07061"],"isi":["000654960800001"]},"article_processing_charge":"No","author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}]},{"year":"2021","isi":1,"publication":"Physical Review B","day":"15","date_created":"2021-06-20T22:01:33Z","date_published":"2021-06-15T00:00:00Z","doi":"10.1103/PhysRevB.103.235201","acknowledgement":"We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","citation":{"mla":"Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:10.1103/PhysRevB.103.235201.","short":"D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021).","ieee":"D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society, 2021.","apa":"Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201","ama":"Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 2021;103(23). doi:10.1103/PhysRevB.103.235201","chicago":"Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201.","ista":"Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["2006.01275"],"isi":["000661512500002"]},"author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"first_name":"E. A.","last_name":"Martinez","full_name":"Martinez, E. A."},{"full_name":"Ménard, G. C.","last_name":"Ménard","first_name":"G. C."},{"first_name":"A.","full_name":"Pöschl, A.","last_name":"Pöschl"},{"first_name":"S.","last_name":"Gronin","full_name":"Gronin, S."},{"first_name":"G. C.","last_name":"Gardner","full_name":"Gardner, G. C."},{"first_name":"R.","full_name":"Kallaher, R.","last_name":"Kallaher"},{"first_name":"M. J.","full_name":"Manfra, M. J.","last_name":"Manfra"},{"first_name":"C. M.","last_name":"Marcus","full_name":"Marcus, C. M."},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casparis, L.","last_name":"Casparis","first_name":"L."}],"title":"Closing of the induced gap in a hybrid superconductor-semiconductor nanowire","article_number":"235201","publication_status":"published","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"language":[{"iso":"eng"}],"volume":103,"related_material":{"record":[{"relation":"research_data","id":"13080","status":"public"}]},"issue":"23","abstract":[{"text":"We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.01275"}],"scopus_import":"1","intvolume":" 103","month":"06","date_updated":"2023-08-08T14:08:08Z","department":[{"_id":"AnHi"}],"_id":"9570","type":"journal_article","article_type":"original","status":"public"},{"external_id":{"arxiv":["2008.09543"],"isi":["000656507500001"]},"article_processing_charge":"No","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory","last_name":"Ivanov"},{"full_name":"Tsiutsiurupa, Igor","last_name":"Tsiutsiurupa","first_name":"Igor"}],"title":"Functional Löwner ellipsoids","citation":{"chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.","ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528.","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.","apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","page":"11493-11528","date_created":"2021-06-13T22:01:32Z","doi":"10.1007/s12220-021-00691-4","date_published":"2021-05-31T00:00:00Z","year":"2021","isi":1,"publication":"Journal of Geometric Analysis","day":"31","type":"journal_article","article_type":"original","status":"public","_id":"9548","department":[{"_id":"UlWa"}],"date_updated":"2023-08-08T14:04:49Z","main_file_link":[{"url":"https://arxiv.org/abs/2008.09543","open_access":"1"}],"scopus_import":"1","intvolume":" 31","month":"05","abstract":[{"lang":"eng","text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it."}],"oa_version":"Preprint","volume":31,"publication_status":"published","publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"language":[{"iso":"eng"}]},{"related_material":{"link":[{"url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3","relation":"software"}],"record":[{"relation":"used_in_publication","id":"9570","status":"public"}]},"doi":"10.5281/ZENODO.4592435","date_published":"2021-03-09T00:00:00Z","date_created":"2023-05-23T17:11:28Z","year":"2021","day":"09","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4592460","open_access":"1"}],"month":"03","abstract":[{"text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"full_name":"Martinez, Esteban","last_name":"Martinez","first_name":"Esteban"},{"last_name":"Menard","full_name":"Menard, Gerbold","first_name":"Gerbold"},{"first_name":"Andreas","full_name":"Pöschl, Andreas","last_name":"Pöschl"},{"last_name":"Gronin","full_name":"Gronin, Sergei","first_name":"Sergei"},{"last_name":"Gardner","full_name":"Gardner, Geoffrey","first_name":"Geoffrey"},{"first_name":"Ray","last_name":"Kallaher","full_name":"Kallaher, Ray"},{"last_name":"Manfra","full_name":"Manfra, Michael","first_name":"Michael"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"},{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"first_name":"Lucas","last_name":"Casparis","full_name":"Casparis, Lucas"}],"article_processing_charge":"No","title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","department":[{"_id":"AnHi"}],"citation":{"short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","ieee":"D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021.","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435","apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435","mla":"Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.","chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435."},"date_updated":"2023-08-08T14:08:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"type":"research_data_reference","status":"public","_id":"13080"},{"acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"day":"18","publication":"RSC Advances","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1039/d1ra03428f","date_published":"2021-06-18T00:00:00Z","date_created":"2021-06-19T07:27:45Z","page":"21702-21715","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021.","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f","ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f","mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:10.1039/d1ra03428f.","ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715.","chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f."},"title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","author":[{"first_name":"M. S.","full_name":"Dar, M. S.","last_name":"Dar"},{"first_name":"Khush Bakhat","full_name":"Akram, Khush Bakhat","last_name":"Akram"},{"full_name":"Sohail, Ayesha","last_name":"Sohail","first_name":"Ayesha"},{"full_name":"Arif, Fatima","last_name":"Arif","first_name":"Fatima"},{"last_name":"Zabihi","full_name":"Zabihi, Fatemeh","first_name":"Fatemeh"},{"full_name":"Yang, Shengyuan","last_name":"Yang","first_name":"Shengyuan"},{"full_name":"Munir, Shamsa","last_name":"Munir","first_name":"Shamsa"},{"full_name":"Zhu, Meifang","last_name":"Zhu","first_name":"Meifang"},{"first_name":"M.","full_name":"Abid, M.","last_name":"Abid"},{"first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad"}],"external_id":{"isi":["000665644000048"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values."}],"month":"06","intvolume":" 11","file":[{"creator":"asandaue","file_size":2114557,"date_updated":"2021-06-23T13:09:34Z","file_name":"2021_RSCAdvances_Dar.pdf","date_created":"2021-06-23T13:09:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"cd582d67ace7151078e46b3a896871a9","file_id":"9596"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2046-2069"]},"publication_status":"published","issue":"35","volume":11,"license":"https://creativecommons.org/licenses/by/3.0/","_id":"9569","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"ddc":["540"],"date_updated":"2023-08-08T14:23:21Z","department":[{"_id":"KiMo"}],"file_date_updated":"2021-06-23T13:09:34Z"},{"title":"Coarse graining the state space of a turbulent flow using periodic orbits","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"}],"article_processing_charge":"No","external_id":{"arxiv":["2007.02584"],"isi":["000663310100008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.","apa":"Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021.","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502."},"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"244502","doi":"10.1103/PhysRevLett.126.244502","date_published":"2021-06-18T00:00:00Z","date_created":"2021-06-16T15:45:36Z","day":"18","publication":"Physical Review Letters","isi":1,"year":"2021","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_updated":"2023-08-08T14:08:36Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"9558","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release"}]},"issue":"24","volume":126,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","month":"06","intvolume":" 126","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.02584"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n"}],"acknowledged_ssus":[{"_id":"ScienComp"}]},{"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","doi":"10.7554/eLife.63294","date_published":"2021-05-24T00:00:00Z","date_created":"2021-06-27T22:01:49Z","day":"24","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2021","title":"Introduction to the EQIPD quality system","author":[{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"first_name":"René","full_name":"Bernard, René","last_name":"Bernard"},{"first_name":"Anja","last_name":"Gilis","full_name":"Gilis, Anja"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"first_name":"Javier","full_name":"Guillén, Javier","last_name":"Guillén"},{"full_name":"Castagné, Vincent","last_name":"Castagné","first_name":"Vincent"},{"last_name":"Lefevre","full_name":"Lefevre, Isabel A.","first_name":"Isabel A."},{"first_name":"Fiona","last_name":"Ducrey","full_name":"Ducrey, Fiona"},{"first_name":"Lee","last_name":"Monk","full_name":"Monk, Lee"},{"first_name":"Sandrine","full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni"},{"full_name":"Altevogt, Bruce","last_name":"Altevogt","first_name":"Bruce"},{"first_name":"María","last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"full_name":"De Bruin, Natasja","last_name":"De Bruin","first_name":"Natasja"},{"first_name":"Esmeralda","last_name":"Castaños-Vélez","full_name":"Castaños-Vélez, Esmeralda"},{"last_name":"Dityatev","full_name":"Dityatev, Alexander","first_name":"Alexander"},{"full_name":"Emmerich, Christoph H.","last_name":"Emmerich","first_name":"Christoph H."},{"first_name":"Raafat","full_name":"Fares, Raafat","last_name":"Fares"},{"full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham","first_name":"Chantelle"},{"last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle","first_name":"Christelle"},{"last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie","first_name":"Valerie"},{"full_name":"Hölter, Sabine M.","last_name":"Hölter","first_name":"Sabine M."},{"first_name":"Martine Cj","full_name":"Hofmann, Martine Cj","last_name":"Hofmann"},{"first_name":"Patricia","last_name":"Kabitzke","full_name":"Kabitzke, Patricia"},{"first_name":"Martien Jh","last_name":"Kas","full_name":"Kas, Martien Jh"},{"full_name":"Kurreck, Claudia","last_name":"Kurreck","first_name":"Claudia"},{"last_name":"Moser","full_name":"Moser, Paul","first_name":"Paul"},{"last_name":"Pietraszek","full_name":"Pietraszek, Malgorzata","first_name":"Malgorzata"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"first_name":"Heidrun","full_name":"Potschka, Heidrun","last_name":"Potschka"},{"first_name":"Ernesto","full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca"},{"last_name":"Restivo","full_name":"Restivo, Leonardo","first_name":"Leonardo"},{"full_name":"Riedel, Gernot","last_name":"Riedel","first_name":"Gernot"},{"first_name":"Merel","last_name":"Ritskes-Hoitinga","full_name":"Ritskes-Hoitinga, Merel"},{"first_name":"Janko","full_name":"Samardzic, Janko","last_name":"Samardzic"},{"orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael","last_name":"Schunn","first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudia","full_name":"Stöger, Claudia","last_name":"Stöger"},{"last_name":"Voikar","full_name":"Voikar, Vootele","first_name":"Vootele"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"first_name":"Kimberley E.","full_name":"Wever, Kimberley E.","last_name":"Wever"},{"last_name":"Wuyts","full_name":"Wuyts, Kathleen","first_name":"Kathleen"},{"last_name":"Macleod","full_name":"Macleod, Malcolm R.","first_name":"Malcolm R."},{"first_name":"Ulrich","last_name":"Dirnagl","full_name":"Dirnagl, Ulrich"},{"last_name":"Steckler","full_name":"Steckler, Thomas","first_name":"Thomas"}],"article_processing_charge":"No","external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294."},"month":"05","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.","lang":"eng"}],"volume":10,"file":[{"creator":"asandaue","file_size":2500720,"date_updated":"2021-06-28T11:35:30Z","file_name":"2021_ELife_Bespalov.pdf","date_created":"2021-06-28T11:35:30Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9609","checksum":"885b746051a7a6b6e24e3d2781a48fde"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9607","department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","ddc":["570"],"date_updated":"2023-08-10T13:36:50Z"},{"_id":"9601","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-10T13:53:23Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-06-28T08:04:22Z","abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 12","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"file_name":"2021_NatureCommunications_Santini.pdf","date_created":"2021-06-28T08:04:22Z","file_size":2156554,"date_updated":"2021-06-28T08:04:22Z","creator":"asandaue","success":1,"checksum":"75dd89d09945185b2d14b2434a0bcb50","file_id":"9608","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":12,"issue":"1","article_number":"3804","citation":{"mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"first_name":"Florian","full_name":"Halbritter, Florian","last_name":"Halbritter"},{"first_name":"Fabian","full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"last_name":"Asami","full_name":"Asami, Maki","first_name":"Maki"},{"first_name":"Xiaoyan","full_name":"Ma, Xiaoyan","last_name":"Ma"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"full_name":"Laue, Ernest","last_name":"Laue","first_name":"Ernest"},{"full_name":"Farlik, Matthias","last_name":"Farlik","first_name":"Matthias"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"last_name":"Beyer","full_name":"Beyer, Andreas","first_name":"Andreas"},{"first_name":"Anthony C.F.","last_name":"Perry","full_name":"Perry, Anthony C.F."},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"}],"article_processing_charge":"No","external_id":{"isi":["000667248600005"]},"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"12","publication":"Nature Communications","doi":"10.1038/s41467-021-23510-4","date_published":"2021-07-12T00:00:00Z","date_created":"2021-06-27T22:01:46Z"},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9602","department":[{"_id":"HeEd"}],"file_date_updated":"2021-06-28T13:33:23Z","date_updated":"2023-08-10T13:38:00Z","ddc":["510"],"scopus_import":"1","month":"06","intvolume":" 151","abstract":[{"lang":"eng","text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees."}],"oa_version":"Published Version","volume":151,"publication_identifier":{"issn":["0095-8956"]},"publication_status":"published","file":[{"date_created":"2021-06-28T13:33:23Z","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","creator":"asandaue","date_updated":"2021-06-28T13:33:23Z","file_size":418168,"file_id":"9612","checksum":"15fbc9064cd9d1c777ac0043b78c8f12","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach","full_name":"Pach, János"},{"last_name":"Tomon","full_name":"Tomon, István","first_name":"István"}],"external_id":{"isi":["000702280800002"]},"article_processing_charge":"No","title":"Erdős-Hajnal-type results for monotone paths","citation":{"ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004.","apa":"Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","page":"21-37","doi":"10.1016/j.jctb.2021.05.004","date_published":"2021-06-09T00:00:00Z","date_created":"2021-06-27T22:01:47Z","isi":1,"has_accepted_license":"1","year":"2021","day":"09","publication":"Journal of Combinatorial Theory. Series B"},{"main_file_link":[{"url":"https://arxiv.org/abs/2009.06491","open_access":"1"}],"scopus_import":"1","intvolume":" 103","month":"06","abstract":[{"lang":"eng","text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results."}],"oa_version":"Preprint","volume":103,"issue":"6","publication_status":"published","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"language":[{"iso":"eng"}],"article_type":"letter_note","type":"journal_article","status":"public","_id":"9606","department":[{"_id":"MiLe"}],"date_updated":"2023-08-10T13:37:25Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","date_created":"2021-06-27T22:01:49Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1103/PhysRevA.103.L061303","year":"2021","isi":1,"publication":"Physical Review A","day":"01","article_number":"L061303","article_processing_charge":"No","external_id":{"isi":["000662296700014"],"arxiv":["2009.06491"]},"author":[{"full_name":"Tononi, A.","last_name":"Tononi","first_name":"A."},{"full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"last_name":"Salasnich","full_name":"Salasnich, L.","first_name":"L."}],"title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","citation":{"ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021.","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303","apa":"Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-07-19T13:32:17Z","file_size":56388540,"creator":"cziletti","date_created":"2021-07-19T13:32:17Z","file_name":"2021_CellReports_Venturino.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f056255f6d01fd9a86b5387635928173","file_id":"9693","success":1}],"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"ec_funded":1,"issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","relation":"press_release","description":"News on IST Homepage"}]},"volume":36,"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.","lang":"eng"}],"intvolume":" 36","month":"07","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-10T14:09:39Z","department":[{"_id":"SaSi"}],"file_date_updated":"2021-07-19T13:32:17Z","_id":"9642","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","publication":"Cell Reports","day":"06","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-07-11T22:01:16Z","doi":"10.1016/j.celrep.2021.109313","date_published":"2021-07-06T00:00:00Z","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313."},"title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","article_processing_charge":"No","external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"author":[{"last_name":"Venturino","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven"},{"full_name":"De Jesús-Cortés, Héctor","last_name":"De Jesús-Cortés","first_name":"Héctor"},{"last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nagy, Balint","last_name":"Nagy","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","first_name":"Balint"},{"last_name":"Reilly-Andújar","full_name":"Reilly-Andújar, Francis","first_name":"Francis"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo"},{"first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867"},{"last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark F.","last_name":"Bear","full_name":"Bear, Mark F."},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"}],"article_number":"109313","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"article_number":"109274","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","last_name":"Contreras"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"first_name":"Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425","last_name":"Davaatseren","full_name":"Davaatseren, Amarbayasgalan"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H"},{"full_name":"Sonntag, Johanna","last_name":"Sonntag","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","first_name":"Johanna"},{"first_name":"Lill","full_name":"Andersen, Lill","last_name":"Andersen"},{"first_name":"Tina","last_name":"Bernthaler","full_name":"Bernthaler, Tina"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","last_name":"Heger","full_name":"Heger, Anna-Magdalena"},{"first_name":"Randy L.","full_name":"Johnson, Randy L.","last_name":"Johnson"},{"full_name":"Schwarz, Lindsay A.","last_name":"Schwarz","first_name":"Lindsay A."},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"external_id":{"isi":["000664463600016"]},"article_processing_charge":"No","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","quality_controlled":"1","publisher":"Cell Press","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"22","publication":"Cell Reports","date_published":"2021-06-22T00:00:00Z","doi":"10.1016/j.celrep.2021.109274","date_created":"2021-06-27T22:01:48Z","_id":"9603","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-08-10T13:55:00Z","ddc":["570"],"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"file_date_updated":"2021-06-28T14:06:24Z","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 35","publication_identifier":{"eissn":["22111247"]},"publication_status":"published","file":[{"file_size":7653149,"date_updated":"2021-06-28T14:06:24Z","creator":"asandaue","file_name":"2021_CellReports_Contreras.pdf","date_created":"2021-06-28T14:06:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77"}],"language":[{"iso":"eng"}],"volume":35,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"issue":"12","ec_funded":1}]