[{"oa":1,"publisher":"Springer Nature","intvolume":"         7","doi":"10.1007/s41468-023-00116-x","page":"619-641","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"type":"journal_article","publication":"Journal of Applied and Computational Topology","oa_version":"Submitted Version","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Boissonnat, Jean Daniel","last_name":"Boissonnat","first_name":"Jean Daniel"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"month":"09","article_type":"original","status":"public","quality_controlled":"1","date_published":"2023-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality."}],"main_file_link":[{"url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1","open_access":"1"}],"publication_status":"published","date_created":"2023-03-26T22:01:08Z","_id":"12763","date_updated":"2023-10-04T12:07:18Z","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"citation":{"ieee":"J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,” <i>Journal of Applied and Computational Topology</i>, vol. 7. Springer Nature, pp. 619–641, 2023.","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>.","ama":"Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. 2023;7:619-641. doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>","mla":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>, vol. 7, Springer Nature, 2023, pp. 619–41, doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>.","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","apa":"Boissonnat, J. D., &#38; Wintraecken, M. (2023). The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>","ista":"Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 7, 619–641."},"department":[{"_id":"HeEd"}],"year":"2023","day":"01","title":"The reach of subsets of manifolds","volume":7,"acknowledgement":"We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu for encouragement. We further acknowledge the anonymous reviewers whose comments helped improve the exposition.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). The first author is further supported by the French government, through the 3IA Côte d’Azur Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-19-P3IA-0002. The second author is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073."},{"volume":70,"acknowledgement":"Open access funding provided by the Austrian Science Fund (FWF). This research was supported by the FWF grant, Project number I4245-N35, and by the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) - Project-ID 195170736 - TRR109.","external_id":{"isi":["000948148000001"]},"day":"01","title":"Discrete yamabe problem for polyhedral surfaces","year":"2023","citation":{"short":"H. Kourimska, Discrete and Computational Geometry 70 (2023) 123–153.","apa":"Kourimska, H. (2023). Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>","ista":"Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 70, 123–153.","chicago":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>.","mla":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>, vol. 70, Springer Nature, 2023, pp. 123–53, doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>.","ama":"Kourimska H. Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. 2023;70:123-153. doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>","ieee":"H. Kourimska, “Discrete yamabe problem for polyhedral surfaces,” <i>Discrete and Computational Geometry</i>, vol. 70. Springer Nature, pp. 123–153, 2023."},"department":[{"_id":"HeEd"}],"_id":"12764","date_updated":"2023-10-04T11:46:48Z","project":[{"_id":"26AD5D90-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245"}],"file_date_updated":"2023-10-04T11:46:24Z","date_created":"2023-03-26T22:01:09Z","publication_status":"published","file":[{"date_created":"2023-10-04T11:46:24Z","relation":"main_file","creator":"dernst","checksum":"cdbf90ba4a7ddcb190d37b9e9d4cb9d3","access_level":"open_access","file_size":1026683,"file_id":"14396","content_type":"application/pdf","success":1,"file_name":"2023_DiscreteGeometry_Kourimska.pdf","date_updated":"2023-10-04T11:46:24Z"}],"date_published":"2023-07-01T00:00:00Z","ddc":["510"],"abstract":[{"lang":"eng","text":"We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique."}],"article_type":"original","status":"public","quality_controlled":"1","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Kourimska","full_name":"Kourimska, Hana","first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091"}],"month":"07","publication":"Discrete and Computational Geometry","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"123-153","doi":"10.1007/s00454-023-00484-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"type":"journal_article","oa":1,"publisher":"Springer Nature","isi":1,"intvolume":"        70","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"language":[{"iso":"eng"}],"publication":"Functional Ecology","oa_version":"None","page":"809-820","doi":"10.1111/1365-2435.14310","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1365-2435"],"issn":["0269-8463"]},"publisher":"British Ecological Society","intvolume":"        37","isi":1,"abstract":[{"text":"Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection.\r\nBecause they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group.\r\nHere, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals.\r\nWe discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies.\r\nFinally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.","lang":"eng"}],"date_published":"2023-04-01T00:00:00Z","status":"public","article_type":"review","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","month":"04","author":[{"first_name":"Sebastian","full_name":"Stockmaier, Sebastian","last_name":"Stockmaier"},{"full_name":"Ulrich, Yuko","last_name":"Ulrich","first_name":"Yuko"},{"first_name":"Gregory F.","full_name":"Albery, Gregory F.","last_name":"Albery"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"first_name":"Patricia C.","full_name":"Lopes, Patricia C.","last_name":"Lopes"}],"department":[{"_id":"SyCr"}],"citation":{"ieee":"S. Stockmaier, Y. Ulrich, G. F. Albery, S. Cremer, and P. C. Lopes, “Behavioural defences against parasites across host social structures,” <i>Functional Ecology</i>, vol. 37, no. 4. British Ecological Society, pp. 809–820, 2023.","short":"S. Stockmaier, Y. Ulrich, G.F. Albery, S. Cremer, P.C. Lopes, Functional Ecology 37 (2023) 809–820.","ista":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. 2023. Behavioural defences against parasites across host social structures. Functional Ecology. 37(4), 809–820.","apa":"Stockmaier, S., Ulrich, Y., Albery, G. F., Cremer, S., &#38; Lopes, P. C. (2023). Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. British Ecological Society. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>","chicago":"Stockmaier, Sebastian, Yuko Ulrich, Gregory F. Albery, Sylvia Cremer, and Patricia C. Lopes. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>. British Ecological Society, 2023. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>.","mla":"Stockmaier, Sebastian, et al. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>, vol. 37, no. 4, British Ecological Society, 2023, pp. 809–20, doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>.","ama":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. 2023;37(4):809-820. doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>"},"date_updated":"2023-10-04T11:50:15Z","_id":"12765","date_created":"2023-03-26T22:01:09Z","publication_status":"published","volume":37,"external_id":{"isi":["000948940500001"]},"title":"Behavioural defences against parasites across host social structures","day":"01","year":"2023","issue":"4"},{"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"page":"127","degree_awarded":"PhD","doi":"10.15479/at:ista:12781","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"12138","status":"public"}]},"publisher":"Institute of Science and Technology Austria","status":"public","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"ddc":["570","572"],"date_published":"2023-03-23T00:00:00Z","file":[{"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_updated":"2023-04-19T14:33:41Z","embargo_to":"local","content_type":"application/pdf","file_id":"12852","file_size":6071553,"access_level":"closed","checksum":"5ebb6345cb4119f93460c81310265a6d","creator":"vkravchu","relation":"main_file","date_created":"2023-04-19T14:33:41Z","embargo":"2024-04-20"},{"date_updated":"2023-04-20T07:02:59Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","embargo_to":"local","file_size":19468766,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12853","creator":"vkravchu","checksum":"c12055c48411d030d2afa51de2166221","embargo":"2024-04-20","relation":"source_file","date_created":"2023-04-19T14:33:52Z"}],"month":"03","author":[{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-04-20T07:02:59Z","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"date_updated":"2023-08-04T08:54:51Z","_id":"12781","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023."},"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-03-31T12:24:42Z","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","day":"23","supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"year":"2023"},{"external_id":{"isi":["001066658700003"]},"day":"25","title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","volume":14,"acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","year":"2023","_id":"12786","date_updated":"2023-12-13T11:15:58Z","file_date_updated":"2023-04-03T06:38:56Z","citation":{"short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>.","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>, vol. 14, 1659, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>.","ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>","ieee":"D. Zhang <i>et al.</i>, “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"department":[{"_id":"PeJo"}],"publication_status":"published","date_created":"2023-04-02T22:01:09Z","article_type":"original","status":"public","quality_controlled":"1","file":[{"checksum":"0a97b31191432dae5853bbb5ccb7698d","creator":"dernst","relation":"main_file","date_created":"2023-04-03T06:38:56Z","file_name":"2023_NatureComm_Zhang.pdf","date_updated":"2023-04-03T06:38:56Z","success":1,"content_type":"application/pdf","file_id":"12797","file_size":2613996,"access_level":"open_access"}],"date_published":"2023-03-25T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators."}],"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Danyang","full_name":"Zhang, Danyang","last_name":"Zhang"},{"first_name":"Remigijus","full_name":"Lape, Remigijus","last_name":"Lape"},{"first_name":"Saher A.","full_name":"Shaikh, Saher A.","last_name":"Shaikh"},{"last_name":"Kohegyi","full_name":"Kohegyi, Bianka K.","first_name":"Bianka K."},{"full_name":"Watson, Jake","last_name":"Watson","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"first_name":"Ondrej","full_name":"Cais, Ondrej","last_name":"Cais"},{"first_name":"Terunaga","last_name":"Nakagawa","full_name":"Nakagawa, Terunaga"},{"first_name":"Ingo H.","last_name":"Greger","full_name":"Greger, Ingo H."}],"month":"03","article_number":"1659","has_accepted_license":"1","doi":"10.1038/s41467-023-37259-5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","publication":"Nature Communications","oa_version":"Published Version","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Springer Nature","isi":1,"intvolume":"        14"},{"year":"2023","issue":"2271","acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","volume":479,"external_id":{"isi":["000957125500002"]},"title":"Coexistence times in the Moran process with environmental heterogeneity","day":"29","date_created":"2023-04-02T22:01:09Z","publication_status":"published","department":[{"_id":"KrCh"}],"citation":{"apa":"Svoboda, J., Tkadlec, J., Kaveh, K., &#38; Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspa.2022.0685\">https://doi.org/10.1098/rspa.2022.0685</a>","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rspa.2022.0685\">10.1098/rspa.2022.0685</a>.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2023;479(2271). doi:<a href=\"https://doi.org/10.1098/rspa.2022.0685\">10.1098/rspa.2022.0685</a>","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2023. <a href=\"https://doi.org/10.1098/rspa.2022.0685\">https://doi.org/10.1098/rspa.2022.0685</a>.","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 479, no. 2271. The Royal Society, 2023."},"date_updated":"2025-07-14T09:09:51Z","_id":"12787","file_date_updated":"2023-04-03T06:25:29Z","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"article_number":"20220685","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","month":"03","author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","first_name":"Jakub","full_name":"Svoboda, Jakub","last_name":"Svoboda"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"last_name":"Kaveh","full_name":"Kaveh, Kamran","first_name":"Kamran"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"file":[{"relation":"main_file","date_created":"2023-04-03T06:25:29Z","checksum":"13953d349fbefcb5d21ccc6b303297eb","creator":"dernst","content_type":"application/pdf","file_id":"12796","file_size":827784,"access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","date_updated":"2023-04-03T06:25:29Z","success":1}],"abstract":[{"lang":"eng","text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results."}],"ddc":["000"],"date_published":"2023-03-29T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","oa":1,"publisher":"The Royal Society","intvolume":"       479","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"related_material":{"link":[{"relation":"research_data","url":"https://doi.org/10.6084/m9.figshare.21261771.v1"}]},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","doi":"10.1098/rspa.2022.0685","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]}},{"article_processing_charge":"No","scopus_import":"1","month":"03","author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","full_name":"Karle, Volker","last_name":"Karle"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"article_number":"103202","status":"public","article_type":"original","quality_controlled":"1","abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"date_published":"2023-03-10T00:00:00Z","oa":1,"publisher":"American Physical Society","intvolume":"       130","isi":1,"doi":"10.1103/PhysRevLett.130.103202","type":"journal_article","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"oa_version":"Preprint","publication":"Physical Review Letters","year":"2023","issue":"10","external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"title":"Topological charges of periodically kicked molecules","day":"10","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","volume":130,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.07067"}],"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T14:02:06Z","_id":"12788","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"department":[{"_id":"MiLe"}],"citation":{"ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","apa":"Karle, V., Ghazaryan, A., &#38; Lemeshko, M. (2023). Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>.","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>.","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023."}},{"department":[{"_id":"ScWa"}],"citation":{"ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","apa":"Mujica, N., &#38; Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>","mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>.","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>.","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” <i>Physical Review E</i>, vol. 107, no. 3. American Physical Society, 2023."},"file_date_updated":"2023-11-27T09:51:48Z","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"}],"date_updated":"2023-11-28T09:22:25Z","_id":"12789","date_created":"2023-04-02T22:01:10Z","publication_status":"published","acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","volume":107,"title":"Accurate determination of the shapes of granular charge distributions","day":"01","external_id":{"isi":["000992142700001"]},"year":"2023","issue":"3","ec_funded":1,"language":[{"iso":"eng"}],"publication":"Physical Review E","oa_version":"Published Version","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.1103/PhysRevE.107.034901","intvolume":"       107","isi":1,"publisher":"American Physical Society","oa":1,"abstract":[{"text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.","lang":"eng"}],"ddc":["530"],"date_published":"2023-03-01T00:00:00Z","file":[{"file_size":1428631,"access_level":"open_access","content_type":"application/pdf","file_id":"14612","success":1,"file_name":"PhysRevE.107.034901 (1).pdf","date_updated":"2023-11-27T09:51:48Z","relation":"main_file","date_created":"2023-11-27T09:51:48Z","creator":"swaituka","checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea"}],"quality_controlled":"1","status":"public","article_type":"original","article_number":"034901","has_accepted_license":"1","month":"03","author":[{"first_name":"Nicolás","full_name":"Mujica, Nicolás","last_name":"Mujica"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"article_processing_charge":"No","scopus_import":"1"},{"status":"public","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity."}],"date_published":"2023-03-01T00:00:00Z","article_processing_charge":"No","scopus_import":"1","month":"03","author":[{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"first_name":"Tobias","full_name":"Holder, Tobias","last_name":"Holder"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"article_number":"104502","doi":"10.1103/PhysRevB.107.104502","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/","relation":"press_release","description":"News on the ISTA website"}]},"language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"publication":"Physical Review B","publisher":"American Physical Society","oa":1,"intvolume":"       107","isi":1,"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","day":"01","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","volume":107,"year":"2023","issue":"10","date_updated":"2023-08-01T13:59:29Z","_id":"12790","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"citation":{"ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” <i>Physical Review B</i>, vol. 107, no. 10. American Physical Society, 2023.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">https://doi.org/10.1103/PhysRevB.107.104502</a>.","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” <i>Physical Review B</i>, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">10.1103/PhysRevB.107.104502</a>.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. <i>Physical Review B</i>. 2023;107(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">10.1103/PhysRevB.107.104502</a>","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","apa":"Ghazaryan, A., Holder, T., Berg, E., &#38; Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">https://doi.org/10.1103/PhysRevB.107.104502</a>","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502."},"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02492"}],"date_created":"2023-04-02T22:01:10Z"},{"title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","day":"20","external_id":{"arxiv":["2301.07769"],"isi":["000956387200001"]},"acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","volume":46,"year":"2023","issue":"3","date_updated":"2023-08-01T14:03:47Z","_id":"12791","department":[{"_id":"CaMu"}],"citation":{"ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” <i>The European Physical Journal E</i>, vol. 46, no. 3. Springer Nature, 2023.","chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” <i>The European Physical Journal E</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">https://doi.org/10.1140/epje/s10189-023-00276-9</a>.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. <i>The European Physical Journal E</i>. 2023;46(3). doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">10.1140/epje/s10189-023-00276-9</a>","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” <i>The European Physical Journal E</i>, vol. 46, no. 3, 16, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">10.1140/epje/s10189-023-00276-9</a>.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., &#38; Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. <i>The European Physical Journal E</i>. Springer Nature. <a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">https://doi.org/10.1140/epje/s10189-023-00276-9</a>"},"publication_status":"published","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2301.07769"}],"date_created":"2023-04-02T22:01:11Z","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"lang":"eng","text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra."}],"date_published":"2023-03-20T00:00:00Z","month":"03","author":[{"full_name":"Clark Di Leoni, Patricio","last_name":"Clark Di Leoni","first_name":"Patricio"},{"id":"cd100965-0804-11ed-9c55-f4878ff4e877","first_name":"Lokahith N","full_name":"Agasthya, Lokahith N","last_name":"Agasthya"},{"full_name":"Buzzicotti, Michele","last_name":"Buzzicotti","first_name":"Michele"},{"first_name":"Luca","last_name":"Biferale","full_name":"Biferale, Luca"}],"article_processing_charge":"No","scopus_import":"1","article_number":"16","type":"journal_article","publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"publication":"The European Physical Journal E","intvolume":"        46","isi":1,"oa":1,"publisher":"Springer Nature"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"page":"1665-1700","doi":"10.1007/s00220-023-04692-y","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Communications in Mathematical Physics","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"       401","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"lang":"eng","text":"In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics."}],"ddc":["510"],"date_published":"2023-07-01T00:00:00Z","file":[{"file_size":859967,"access_level":"open_access","content_type":"application/pdf","file_id":"14397","success":1,"date_updated":"2023-10-04T12:09:18Z","file_name":"2023_CommMathPhysics_Cipolloni.pdf","relation":"main_file","date_created":"2023-10-04T12:09:18Z","creator":"dernst","checksum":"72057940f76654050ca84a221f21786c"}],"month":"07","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","has_accepted_license":"1","file_date_updated":"2023-10-04T12:09:18Z","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"date_updated":"2023-10-04T12:10:31Z","_id":"12792","department":[{"_id":"LaEr"}],"citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “On the spectral form factor for random matrices,” <i>Communications in Mathematical Physics</i>, vol. 401. Springer Nature, pp. 1665–1700, 2023.","mla":"Cipolloni, Giorgio, et al. “On the Spectral Form Factor for Random Matrices.” <i>Communications in Mathematical Physics</i>, vol. 401, Springer Nature, 2023, pp. 1665–700, doi:<a href=\"https://doi.org/10.1007/s00220-023-04692-y\">10.1007/s00220-023-04692-y</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. On the spectral form factor for random matrices. <i>Communications in Mathematical Physics</i>. 2023;401:1665-1700. doi:<a href=\"https://doi.org/10.1007/s00220-023-04692-y\">10.1007/s00220-023-04692-y</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Spectral Form Factor for Random Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00220-023-04692-y\">https://doi.org/10.1007/s00220-023-04692-y</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). On the spectral form factor for random matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-023-04692-y\">https://doi.org/10.1007/s00220-023-04692-y</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random matrices. Communications in Mathematical Physics. 401, 1665–1700.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 401 (2023) 1665–1700."},"publication_status":"published","date_created":"2023-04-02T22:01:11Z","title":"On the spectral form factor for random matrices","day":"01","external_id":{"isi":["000957343500001"]},"acknowledgement":"We are grateful to the authors of [25] for sharing with us their insights and preliminary numerical results. We are especially thankful to Stephen Shenker for very valuable advice over several email communications. Helpful comments on the manuscript from Peter Forrester and from the anonymous referees are also acknowledged.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nLászló Erdős: Partially supported by ERC Advanced Grant \"RMTBeyond\" No. 101020331. Dominik Schröder: Supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","volume":401,"year":"2023"},{"alternative_title":["ISTA Master's Thesis"],"publication_status":"published","date_created":"2023-04-04T18:57:11Z","date_updated":"2023-06-02T22:30:05Z","_id":"12800","file_date_updated":"2023-06-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023."},"year":"2023","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","day":"05","publisher":"Institute of Science and Technology Austria","oa":1,"page":"21","doi":"10.15479/at:ista:12800","degree_awarded":"MS","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","month":"04","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","full_name":"Julseth, Mara","last_name":"Julseth"}],"has_accepted_license":"1","status":"public","file":[{"date_updated":"2023-06-02T22:30:04Z","file_name":"Dispersaldata.xlsx","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"12805","file_size":52795,"access_level":"closed","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","creator":"mjulseth","relation":"supplementary_material","date_created":"2023-04-06T06:09:40Z"},{"content_type":"application/vnd.wolfram.nb","file_id":"12806","file_size":787239,"access_level":"open_access","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z","relation":"supplementary_material","date_created":"2023-04-06T06:11:27Z","embargo":"2023-06-01","checksum":"5a13b6d204371572e249f03795bc0d04","creator":"mjulseth"},{"access_level":"closed","file_size":1061763,"file_id":"12812","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.docx","date_created":"2023-04-06T08:26:12Z","relation":"source_file","creator":"mjulseth","checksum":"c3ec842839ed1e66bf2618ae33047df8"},{"file_name":"ThesisMaraJulseth_04_23.pdf","date_updated":"2023-06-02T22:30:04Z","file_id":"12813","content_type":"application/pdf","access_level":"open_access","file_size":1741364,"checksum":"3132cc998fbe3ae2a3a83c2a69367f37","creator":"mjulseth","date_created":"2023-04-06T08:26:37Z","relation":"main_file","embargo":"2023-06-01"}],"ddc":["576"],"abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"date_published":"2023-04-05T00:00:00Z"},{"year":"2023","issue":"9","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","volume":186,"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","day":"27","external_id":{"isi":["000991468700001"]},"date_created":"2023-04-05T08:15:40Z","publication_status":"published","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"citation":{"ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>"},"file_date_updated":"2023-05-02T09:26:21Z","project":[{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"}],"date_updated":"2024-02-07T08:03:32Z","_id":"12802","has_accepted_license":"1","month":"04","author":[{"last_name":"Knaus","full_name":"Knaus, Lisa","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico"},{"first_name":"Daniel","full_name":"Malzl, Daniel","last_name":"Malzl"},{"first_name":"Maria","last_name":"Gerykova Bujalkova","full_name":"Gerykova Bujalkova, Maria"},{"full_name":"Smogavec, Mateja","last_name":"Smogavec","first_name":"Mateja"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A.","first_name":"Lena A."},{"last_name":"Gorkiewicz","full_name":"Gorkiewicz, Sarah","first_name":"Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole"},{"full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Christian","last_name":"Knittl-Frank","full_name":"Knittl-Frank, Christian"},{"first_name":"Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","last_name":"Tassinari","full_name":"Tassinari, Marianna"},{"last_name":"Maulide","full_name":"Maulide, Nuno","first_name":"Nuno"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"last_name":"Menche","full_name":"Menche, Jörg","first_name":"Jörg"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"date_published":"2023-04-27T00:00:00Z","file":[{"file_size":15712841,"access_level":"open_access","content_type":"application/pdf","file_id":"12889","success":1,"file_name":"2023_Cell_Knaus.pdf","date_updated":"2023-05-02T09:26:21Z","relation":"main_file","date_created":"2023-05-02T09:26:21Z","creator":"dernst","checksum":"47e94fbe19e86505b429cb7a5b503ce6"}],"quality_controlled":"1","status":"public","article_type":"original","intvolume":"       186","isi":1,"oa":1,"publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ec_funded":1,"language":[{"iso":"eng"}],"publication":"Cell","oa_version":"Published Version","related_material":{"record":[{"id":"13107","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}]},"type":"journal_article","publication_identifier":{"issn":["0092-8674"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.cell.2023.02.037","page":"1950-1967.e25"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.15479/at:ista:12809","page":"115","degree_awarded":"PhD","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663 - 337X"]},"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"12814","content_type":"application/pdf","access_level":"closed","file_size":9881969,"embargo_to":"open_access","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_updated":"2023-04-07T06:16:06Z","date_created":"2023-04-07T06:16:06Z","relation":"main_file","embargo":"2024-04-07","checksum":"35b5997d2b0acb461f9d33d073da0df5","creator":"cchlebak"},{"checksum":"81198f63c294890f6d58e8b29782efdc","creator":"cchlebak","relation":"source_file","date_created":"2023-04-07T06:17:11Z","date_updated":"2023-04-07T06:17:11Z","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","content_type":"application/pdf","file_id":"12815","file_size":44201583,"access_level":"closed"},{"creator":"cchlebak","checksum":"0317bf7f457bb585f99d453ffa69eb53","date_created":"2023-04-07T06:18:05Z","relation":"source_file","file_name":"Thesis_CatarinaAlcarva_final.docx","date_updated":"2023-04-07T06:18:05Z","access_level":"closed","file_size":84731244,"file_id":"12816","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"ddc":["570"],"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"date_published":"2023-04-06T00:00:00Z","status":"public","has_accepted_license":"1","article_processing_charge":"No","month":"04","author":[{"last_name":"Alcarva","full_name":"Alcarva, Catarina","first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"citation":{"ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023."},"date_updated":"2023-04-26T12:16:56Z","_id":"12809","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"file_date_updated":"2023-04-07T06:18:05Z","date_created":"2023-04-06T07:54:09Z","alternative_title":["ISTA Thesis"],"publication_status":"published","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","day":"06","year":"2023","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}]},{"article_processing_charge":"No","month":"05","author":[{"full_name":"Danzl, Johann 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Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ","abstract":[{"text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"ddc":["570"],"date_published":"2023-05-19T00:00:00Z","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png"},"date_created":"2023-04-07T11:37:40Z","oa":1,"publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_updated":"2024-01-10T08:37:48Z","_id":"12817","doi":"10.15479/AT:ISTA:12817","type":"research_data","contributor":[{"last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp"},{"last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"last_name":"Wei","first_name":"Donglai"},{"first_name":"Zudi","last_name":"Lin"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson"},{"last_name":"Troidl","first_name":"Jakob"},{"last_name":"Beyer","first_name":"Johanna"},{"last_name":"Ben Simon","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G. N. ","last_name":"Grant"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"first_name":"Hanspeter","last_name":"Pfister"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"file_date_updated":"2023-05-18T19:51:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13267"}]},"department":[{"_id":"JoDa"}],"oa_version":"Published Version","citation":{"ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","short":"J.G. Danzl, (2023).","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>.","mla":"Danzl, Johann G. <i>Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>"}},{"title":"Curvature induces active velocity waves in rotating spherical tissues","day":"24","external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","volume":14,"year":"2023","file_date_updated":"2023-04-11T06:27:00Z","date_updated":"2023-08-01T14:05:30Z","_id":"12818","department":[{"_id":"EdHa"}],"citation":{"ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., &#38; Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>, vol. 14, 1643, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>.","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>."},"publication_status":"published","pmid":1,"date_created":"2023-04-09T22:01:00Z","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues.","lang":"eng"}],"ddc":["570"],"date_published":"2023-03-24T00:00:00Z","file":[{"date_created":"2023-04-11T06:27:00Z","relation":"main_file","creator":"dernst","checksum":"54f06f9eee11d43bab253f3492c983ba","access_level":"open_access","file_size":4146777,"file_id":"12821","content_type":"application/pdf","success":1,"file_name":"2023_NatureComm_Brandstaetter.pdf","date_updated":"2023-04-11T06:27:00Z"}],"month":"03","author":[{"full_name":"Brandstätter, Tom","last_name":"Brandstätter","first_name":"Tom"},{"last_name":"Brückner","full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"last_name":"Han","full_name":"Han, Yu Long","first_name":"Yu Long"},{"first_name":"Ricard","full_name":"Alert, Ricard","last_name":"Alert"},{"first_name":"Ming","last_name":"Guo","full_name":"Guo, Ming"},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."}],"article_processing_charge":"No","scopus_import":"1","has_accepted_license":"1","article_number":"1643","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-023-37054-2","language":[{"iso":"eng"}],"publication":"Nature Communications","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        14","isi":1,"oa":1,"publisher":"Springer Nature"},{"_id":"12819","date_updated":"2023-08-01T14:06:05Z","citation":{"ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” <i>Physical Review A</i>, vol. 107, no. 3. American Physical Society, 2023.","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. <i>Physical Review A</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">10.1103/PhysRevA.107.L031701</a>","mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” <i>Physical Review A</i>, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">10.1103/PhysRevA.107.L031701</a>.","chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">https://doi.org/10.1103/PhysRevA.107.L031701</a>.","ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701.","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., &#38; Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">https://doi.org/10.1103/PhysRevA.107.L031701</a>","short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023)."},"department":[{"_id":"JoFi"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2209.05165"}],"date_created":"2023-04-09T22:01:00Z","day":"22","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","external_id":{"arxiv":["2209.05165"],"isi":["000957799000006"]},"volume":107,"acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","issue":"3","year":"2023","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","doi":"10.1103/PhysRevA.107.L031701","arxiv":1,"oa_version":"Preprint","publication":"Physical Review A","language":[{"iso":"eng"}],"isi":1,"intvolume":"       107","publisher":"American Physical Society","oa":1,"quality_controlled":"1","article_type":"letter_note","status":"public","date_published":"2023-03-22T00:00:00Z","abstract":[{"text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds.","lang":"eng"}],"author":[{"full_name":"Sokolova, Alesya","last_name":"Sokolova","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","orcid":"0000-0002-8308-4144","first_name":"Alesya"},{"full_name":"Kalacheva, D. A.","last_name":"Kalacheva","first_name":"D. A."},{"first_name":"G. P.","full_name":"Fedorov, G. P.","last_name":"Fedorov"},{"last_name":"Astafiev","full_name":"Astafiev, O. V.","first_name":"O. V."}],"month":"03","scopus_import":"1","article_processing_charge":"No","article_number":"L031701"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"oa":1,"date_created":"2023-04-10T05:55:56Z","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.15479/AT:ISTA:12820","_id":"12820","date_updated":"2023-08-01T14:48:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"first_name":"Laura","contributor_type":"researcher","last_name":"Troussicot"},{"last_name":"Burmann","contributor_type":"researcher","first_name":"Björn M."}],"file_date_updated":"2023-04-14T09:39:58Z","type":"research_data","related_material":{"record":[{"id":"13095","relation":"used_in_publication","status":"public"}]},"oa_version":"Published Version","citation":{"ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">https://doi.org/10.15479/AT:ISTA:12820</a>","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>.","short":"P. Schanda, (2023).","mla":"Schanda, Paul. <i>Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>","chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">https://doi.org/10.15479/AT:ISTA:12820</a>."},"department":[{"_id":"PaSc"}],"article_processing_charge":"No","author":[{"last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"month":"04","year":"2023","has_accepted_license":"1","status":"public","day":"18","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","file":[{"success":1,"file_name":"data_deposition.zip","date_updated":"2023-04-14T09:39:33Z","access_level":"open_access","file_size":54184807,"file_id":"12823","content_type":"application/zip","creator":"pschanda","checksum":"54a619605e44c871214fb0e07b05c6bf","date_created":"2023-04-14T09:39:33Z","relation":"main_file"},{"creator":"pschanda","checksum":"8dede9fc78399d13144eb05c62bf5750","relation":"main_file","date_created":"2023-04-14T09:39:58Z","success":1,"file_name":"README","date_updated":"2023-04-14T09:39:58Z","file_size":4978,"access_level":"open_access","content_type":"application/octet-stream","file_id":"12824"}],"date_published":"2023-04-18T00:00:00Z","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}],"ddc":["570"]},{"oa_version":"Published Version","arxiv":1,"publication":"Advanced Intelligent Systems","language":[{"iso":"eng"}],"doi":"10.1002/aisy.202200129","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2640-4567"]},"type":"journal_article","publisher":"Wiley","oa":1,"isi":1,"intvolume":"         5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"relation":"main_file","date_created":"2023-04-17T06:44:17Z","checksum":"d48fc41d39892e7fa0d44cb352dd46aa","creator":"dernst","content_type":"application/pdf","file_id":"12840","file_size":2414125,"access_level":"open_access","date_updated":"2023-04-17T06:44:17Z","file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","success":1}],"date_published":"2023-01-01T00:00:00Z","ddc":["530"],"abstract":[{"lang":"eng","text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter."}],"article_type":"original","status":"public","quality_controlled":"1","has_accepted_license":"1","article_number":"2200129","article_processing_charge":"No","author":[{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","full_name":"Martinet, Quentin","last_name":"Martinet"},{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"month":"01","citation":{"ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” <i>Advanced Intelligent Systems</i>, vol. 5, no. 1. Wiley, 2023.","ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. <i>Advanced Intelligent Systems</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1002/aisy.202200129\">10.1002/aisy.202200129</a>","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” <i>Advanced Intelligent Systems</i>, vol. 5, no. 1, 2200129, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/aisy.202200129\">10.1002/aisy.202200129</a>.","chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” <i>Advanced Intelligent Systems</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/aisy.202200129\">https://doi.org/10.1002/aisy.202200129</a>.","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","apa":"Martinet, Q., Aubret, A., &#38; Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. <i>Advanced Intelligent Systems</i>. Wiley. <a href=\"https://doi.org/10.1002/aisy.202200129\">https://doi.org/10.1002/aisy.202200129</a>","short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023)."},"department":[{"_id":"JePa"}],"_id":"12822","date_updated":"2023-08-01T14:06:50Z","file_date_updated":"2023-04-17T06:44:17Z","date_created":"2023-04-12T08:30:03Z","publication_status":"published","volume":5,"acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","external_id":{"arxiv":["2201.03333"],"isi":["000852291200001"]},"day":"01","title":"Rotation control, interlocking, and self‐positioning of active cogwheels","issue":"1","year":"2023"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","page":"106","doi":"10.15479/at:ista:12826","degree_awarded":"PhD","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","date_published":"2023-04-18T00:00:00Z","ddc":["570","571"],"abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"file":[{"relation":"source_file","date_created":"2023-04-20T09:14:38Z","creator":"vpokusae","checksum":"5f589a9af025f7eeebfd0c186209913e","file_size":14507243,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12857","file_name":"Thesis_Pokusaeva.docx","date_updated":"2023-04-20T09:26:51Z"},{"date_updated":"2023-04-20T09:14:44Z","file_name":"Thesis_Pokusaeva.pdf","success":1,"file_id":"12858","content_type":"application/pdf","access_level":"open_access","file_size":10090711,"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","creator":"vpokusae","date_created":"2023-04-20T09:14:44Z","relation":"main_file"}],"author":[{"first_name":"Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria"}],"month":"04","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-04-20T09:26:51Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"12826","date_updated":"2023-06-23T09:47:36Z","citation":{"ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>","mla":"Pokusaeva, Victoria. <i>Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>.","apa":"Pokusaeva, V. (2023). <i>Neural control of optic flow-based navigation in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023."},"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-04-14T14:56:04Z","day":"18","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","supervisor":[{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"year":"2023"}]