[{"publication_identifier":{"issn":["1422-6928"],"eissn":["1422-6952"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/s00021-023-00803-w","quality_controlled":"1","isi":1,"oa":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"},"external_id":{"arxiv":["2301.12834"],"isi":["001040354900001"]},"file_date_updated":"2023-08-14T07:24:17Z","article_number":"72","volume":25,"date_updated":"2023-12-13T12:08:08Z","date_created":"2023-08-13T22:01:13Z","author":[{"full_name":"Bulíček, Miroslav","first_name":"Miroslav","last_name":"Bulíček"},{"first_name":"Josef","last_name":"Málek","full_name":"Málek, Josef"},{"full_name":"Maringová, Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","last_name":"Maringová","first_name":"Erika"}],"department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","citation":{"ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","apa":"Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer Nature. https://doi.org/10.1007/s00021-023-00803-w","ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer Nature, 2023.","ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w","chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics. Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature, 2023, doi:10.1007/s00021-023-00803-w.","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023)."},"publication":"Journal of Mathematical Fluid Mechanics","issue":"3","abstract":[{"text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2023-08-14T07:24:17Z","date_updated":"2023-08-14T07:24:17Z","checksum":"c549cd8f0dd02ed60477a05ca045f481","success":1,"relation":"main_file","file_id":"14046","content_type":"application/pdf","file_size":845748,"creator":"dernst","file_name":"2023_JourMathFluidMech_Bulicek.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 25","status":"public","ddc":["510"],"title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","_id":"14042","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2023-08-04T00:00:00Z","article_type":"original","citation":{"ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7."},"publication":"Communications Biology","article_processing_charge":"Yes","has_accepted_license":"1","day":"04","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14045","checksum":"1f9324f736bdbb76426b07736651c4cd","success":1,"date_updated":"2023-08-14T07:17:36Z","date_created":"2023-08-14T07:17:36Z","access_level":"open_access","file_name":"2023_CommBiology_Mehes.pdf","content_type":"application/pdf","file_size":10181997,"creator":"dernst"}],"intvolume":" 6","ddc":["570"],"status":"public","title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","_id":"14041","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s42003-023-05181-7","isi":1,"quality_controlled":"1","oa":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"},"external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"publication_identifier":{"eissn":["2399-3642"]},"month":"08","volume":6,"date_created":"2023-08-13T22:01:13Z","date_updated":"2023-12-13T12:07:33Z","author":[{"last_name":"Méhes","first_name":"Elod","full_name":"Méhes, Elod"},{"full_name":"Mones, Enys","first_name":"Enys","last_name":"Mones"},{"full_name":"Varga, Máté","last_name":"Varga","first_name":"Máté"},{"full_name":"Zsigmond, Áron","first_name":"Áron","last_name":"Zsigmond"},{"full_name":"Biri-Kovács, Beáta","first_name":"Beáta","last_name":"Biri-Kovács"},{"first_name":"László","last_name":"Nyitray","full_name":"Nyitray, László"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"}],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","file_date_updated":"2023-08-14T07:17:36Z","article_number":"817"},{"day":"07","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2023-08-07T00:00:00Z","publication":"Developmental Cell","citation":{"apa":"Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001","ieee":"T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform that organizes cellular and biochemical processes,” Developmental Cell, vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.","ista":"Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332.","ama":"Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332. doi:10.1016/j.devcel.2023.06.001","chicago":"Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001.","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.","mla":"Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15, Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001."},"article_type":"original","page":"1315-1332","abstract":[{"text":"Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.","lang":"eng"}],"issue":"15","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"14049","relation":"main_file","date_updated":"2023-08-14T07:57:55Z","date_created":"2023-08-14T07:57:55Z","success":1,"checksum":"d8c5dc97cd40c26da2ec98ae723ab368","file_name":"2023_DevelopmentalCell_Leonard.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3184217}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14039","status":"public","title":"The membrane surface as a platform that organizes cellular and biochemical processes","ddc":["570"],"intvolume":" 58","month":"08","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"doi":"10.1016/j.devcel.2023.06.001","language":[{"iso":"eng"}],"external_id":{"pmid":["37419118"],"isi":["001059110400001"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthetic and structural biology of Rab GTPase networks","_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","grant_number":"101045340"}],"file_date_updated":"2023-08-14T07:57:55Z","author":[{"first_name":"Thomas A.","last_name":"Leonard","full_name":"Leonard, Thomas A."},{"full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Martens, Sascha","last_name":"Martens","first_name":"Sascha"}],"date_updated":"2023-12-13T12:09:20Z","date_created":"2023-08-13T22:01:12Z","volume":58,"year":"2023","acknowledgement":"We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B, and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 101045340 to M.L.). We are grateful for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic, Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaLo"}]},{"scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Nature Communications","citation":{"ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6."},"article_type":"original","date_published":"2023-08-04T00:00:00Z","type":"journal_article","abstract":[{"text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14040","title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","status":"public","ddc":["570"],"intvolume":" 14","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2315325,"file_name":"2023_NatureComm_Zhao.pdf","access_level":"open_access","date_updated":"2023-08-14T07:01:12Z","date_created":"2023-08-14T07:01:12Z","success":1,"checksum":"3b9043df3d51c300f9be95eac3ff9d0b","file_id":"14044","relation":"main_file"}],"oa_version":"Published Version","month":"08","publication_identifier":{"eissn":["2041-1723"]},"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,"external_id":{"isi":["001042606700004"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-40388-6","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"article_number":"4681","file_date_updated":"2023-08-14T07:01:12Z","acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"author":[{"last_name":"Zhao","first_name":"Ziyu","full_name":"Zhao, Ziyu"},{"full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino","first_name":"Irene"},{"last_name":"Knoppová","first_name":"Jana","full_name":"Knoppová, Jana"},{"full_name":"Sobotka, Roman","last_name":"Sobotka","first_name":"Roman"},{"last_name":"Murray","first_name":"James W.","full_name":"Murray, James W."},{"last_name":"Nixon","first_name":"Peter J.","full_name":"Nixon, Peter J."},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"full_name":"Komenda, Josef","last_name":"Komenda","first_name":"Josef"}],"date_updated":"2023-12-13T12:06:56Z","date_created":"2023-08-13T22:01:13Z","volume":14},{"year":"2023","acknowledgement":"This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”.","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias"},{"full_name":"Weininger, Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881","first_name":"Maximilian","last_name":"Weininger"}],"volume":2023,"date_updated":"2023-12-13T12:06:10Z","date_created":"2023-08-06T22:01:10Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.09930","open_access":"1"}],"external_id":{"isi":["001036707700042"],"arxiv":["2304.09930"]},"isi":1,"quality_controlled":"1","doi":"10.1109/LICS56636.2023.10175771","conference":{"name":"LICS: Symposium on Logic in Computer Science","end_date":"2023-06-29","location":"Boston, MA, United States","start_date":"2023-06-26"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798350335873"],"issn":["1043-6871"]},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13967","intvolume":" 2023","title":"Stopping criteria for value iteration on stochastic games with quantitative objectives","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"text":"A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution.","lang":"eng"}],"citation":{"apa":"Kretinsky, J., Meggendorfer, T., & Weininger, M. (2023). Stopping criteria for value iteration on stochastic games with quantitative objectives. In 38th Annual ACM/IEEE Symposium on Logic in Computer Science (Vol. 2023). Boston, MA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS56636.2023.10175771","ieee":"J. Kretinsky, T. Meggendorfer, and M. Weininger, “Stopping criteria for value iteration on stochastic games with quantitative objectives,” in 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Boston, MA, United States, 2023, vol. 2023.","ista":"Kretinsky J, Meggendorfer T, Weininger M. 2023. Stopping criteria for value iteration on stochastic games with quantitative objectives. 38th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science vol. 2023.","ama":"Kretinsky J, Meggendorfer T, Weininger M. Stopping criteria for value iteration on stochastic games with quantitative objectives. In: 38th Annual ACM/IEEE Symposium on Logic in Computer Science. Vol 2023. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/LICS56636.2023.10175771","chicago":"Kretinsky, Jan, Tobias Meggendorfer, and Maximilian Weininger. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” In 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Vol. 2023. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LICS56636.2023.10175771.","short":"J. Kretinsky, T. Meggendorfer, M. Weininger, in:, 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2023.","mla":"Kretinsky, Jan, et al. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” 38th Annual ACM/IEEE Symposium on Logic in Computer Science, vol. 2023, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/LICS56636.2023.10175771."},"publication":"38th Annual ACM/IEEE Symposium on Logic in Computer Science","date_published":"2023-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"publication":"Current Opinion in Genetics and Development","citation":{"chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development, vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.","apa":"Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” Current Opinion in Genetics and Development, vol. 81, no. 8. Elsevier, 2023.","ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087.","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087"},"article_type":"original","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","_id":"13965","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","ddc":["570"],"status":"public","intvolume":" 81","file":[{"access_level":"open_access","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","content_type":"application/pdf","file_size":2568632,"creator":"dernst","relation":"main_file","file_id":"13980","checksum":"a294cd9506b80ed6ef218ef44ed32765","success":1,"date_updated":"2023-08-07T08:32:26Z","date_created":"2023-08-07T08:32:26Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations."}],"issue":"8","external_id":{"isi":["001047020200001"],"pmid":["37441873"]},"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,"quality_controlled":"1","isi":1,"doi":"10.1016/j.gde.2023.102087","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"year":"2023","pmid":1,"department":[{"_id":"DaZi"}],"publisher":"Elsevier","author":[{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","last_name":"Hollwey","first_name":"Elizabeth","full_name":"Hollwey, Elizabeth"},{"last_name":"Briffa","first_name":"Amy","full_name":"Briffa, Amy"},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"}],"date_updated":"2023-12-13T12:05:31Z","date_created":"2023-08-06T22:01:10Z","volume":81,"article_number":"102087","file_date_updated":"2023-08-07T08:32:26Z"},{"doi":"10.15479/at:ista:14058","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"degree_awarded":"PhD","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,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"month":"08","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"id":"12933","relation":"research_data","status":"public"},{"id":"6831","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14077"}]},"author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"}],"date_updated":"2023-12-13T12:15:36Z","date_created":"2023-08-15T10:20:40Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2023-08-18T10:47:55Z","date_published":"2023-08-15T00:00:00Z","citation":{"ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058."},"page":"230","article_processing_charge":"No","has_accepted_license":"1","day":"15","oa_version":"Published Version","file":[{"date_created":"2023-08-16T18:15:17Z","date_updated":"2023-08-17T06:55:24Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","relation":"source_file","file_id":"14075","file_size":10891454,"content_type":"application/zip","creator":"gpuixeus","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed"},{"access_level":"open_access","file_name":"PhDThesis_PuixeuG.pdf","creator":"gpuixeus","content_type":"application/pdf","file_size":19856686,"file_id":"14079","relation":"main_file","success":1,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_created":"2023-08-18T10:47:55Z","date_updated":"2023-08-18T10:47:55Z"}],"_id":"14058","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","status":"public","ddc":["576"],"abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"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,"external_id":{"isi":["001002997200001"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1093/g3journal/jkad121","month":"08","publication_identifier":{"issn":["2160-1836"]},"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","year":"2023","date_created":"2023-08-18T06:52:14Z","date_updated":"2023-12-13T12:15:37Z","volume":13,"author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"12933"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2023-11-07T09:00:19Z","ec_funded":1,"article_type":"original","publication":"G3: Genes, Genomes, Genetics","citation":{"ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","apa":"Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121.","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023)."},"date_published":"2023-08-01T00:00:00Z","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14077","file":[{"creator":"dernst","file_size":845642,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_G3_Puixeu.pdf","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z","file_id":"14498","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns."}],"issue":"8"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","publication":"Journal of Cell Science","citation":{"chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.260668.","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023).","mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:10.1242/jcs.260668.","ieee":"T. Higashi et al., “ZnUMBA - a live imaging method to detect local barrier breaches,” Journal of Cell Science, vol. 136, no. 15. The Company of Biologists, 2023.","apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260668","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 2023;136(15). doi:10.1242/jcs.260668"},"article_type":"original","abstract":[{"text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision.","lang":"eng"}],"issue":"15","type":"journal_article","file":[{"relation":"main_file","embargo":"2024-08-10","file_id":"14092","date_updated":"2023-08-21T07:37:54Z","date_created":"2023-08-21T07:37:54Z","checksum":"a399389b7e3d072f1788b63e612a10b3","embargo_to":"open_access","file_name":"2023_JourCellScience_Higashi.pdf","access_level":"closed","content_type":"application/pdf","file_size":18665315,"creator":"dernst"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14082","ddc":["570"],"title":"ZnUMBA - a live imaging method to detect local barrier breaches","status":"public","intvolume":" 136","month":"08","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"doi":"10.1242/jcs.260668","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001070149000001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-08-21T07:37:54Z","ec_funded":1,"article_number":"jcs260668","author":[{"full_name":"Higashi, Tomohito","last_name":"Higashi","first_name":"Tomohito"},{"first_name":"Rachel E.","last_name":"Stephenson","full_name":"Stephenson, Rachel E."},{"last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"},{"first_name":"Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"},{"first_name":"Atsuko Y.","last_name":"Higashi","full_name":"Higashi, Atsuko Y."},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Chiba, Hideki","first_name":"Hideki","last_name":"Chiba"},{"first_name":"Ann L.","last_name":"Miller","full_name":"Miller, Ann L."}],"date_updated":"2023-12-13T12:11:18Z","date_created":"2023-08-20T22:01:13Z","volume":136,"acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","year":"2023","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"publisher":"The Company of Biologists"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains."}],"intvolume":" 11","title":"Practical limitations of Ethereum’s layer-2","ddc":["000"],"status":"public","_id":"13988","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"checksum":"4b80b0ff212edf7e5842fbdd53784432","date_updated":"2023-08-22T06:37:48Z","date_created":"2023-08-22T06:37:48Z","file_id":"14166","relation":"main_file","creator":"dernst","file_size":1289285,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_IEEEAccess_Neiheiser.pdf"}],"oa_version":"Published Version","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","page":"8651-8662","article_type":"original","citation":{"ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 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PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale.","year":"2023","volume":11,"date_created":"2023-08-09T12:09:57Z","date_updated":"2023-12-13T12:14:52Z","author":[{"first_name":"Ray","last_name":"Neiheiser","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","orcid":"0000-0001-7227-8309","full_name":"Neiheiser, Ray"},{"full_name":"Inacio, Gustavo","first_name":"Gustavo","last_name":"Inacio"},{"last_name":"Rech","first_name":"Luciana","full_name":"Rech, Luciana"},{"full_name":"Montez, Carlos","first_name":"Carlos","last_name":"Montez"},{"full_name":"Matos, Miguel","last_name":"Matos","first_name":"Miguel"},{"last_name":"Rodrigues","first_name":"Luis","full_name":"Rodrigues, Luis"}],"publication_identifier":{"issn":["2169-3536"]},"month":"08","quality_controlled":"1","isi":1,"external_id":{"isi":["000927831000001"]},"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,"language":[{"iso":"eng"}],"doi":"10.1109/access.2023.3237897"},{"file":[{"success":1,"checksum":"0ba0bcd0bb8b18d84792136a4370df90","date_updated":"2023-05-10T09:41:43Z","date_created":"2023-05-10T09:41:43Z","file_id":"12934","relation":"main_file","creator":"gpuixeus","file_size":8029982,"content_type":"text/csv","access_level":"open_access","file_name":"Dataset_S1.csv"},{"file_name":"Dataset_S2.csv","access_level":"open_access","creator":"gpuixeus","content_type":"text/csv","file_size":13667640,"file_id":"12935","relation":"main_file","date_created":"2023-05-10T09:41:43Z","date_updated":"2023-05-10T09:41:43Z","success":1,"checksum":"a62aa9a6d4904e0fdb699cf752640863"},{"file_size":8369141,"content_type":"text/csv","creator":"gpuixeus","file_name":"Dataset_S3.csv","access_level":"open_access","date_created":"2023-05-10T09:41:48Z","date_updated":"2023-05-10T09:41:48Z","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","success":1,"relation":"main_file","file_id":"12936"},{"success":1,"checksum":"f6156e5fc44446c907ddd0d7289d4cf8","date_updated":"2023-05-10T09:41:50Z","date_created":"2023-05-10T09:41:50Z","file_id":"12937","relation":"main_file","creator":"gpuixeus","file_size":19543247,"content_type":"text/csv","access_level":"open_access","file_name":"Dataset_S4.csv"},{"date_updated":"2023-05-11T12:50:18Z","date_created":"2023-05-11T12:50:18Z","success":1,"checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_id":"12944","relation":"main_file","creator":"gpuixeus","content_type":"text/plain","file_size":4566,"file_name":"readme.txt","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2023-12-13T12:15:36Z","date_created":"2023-05-10T10:00:49Z","contributor":[{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14058"},{"relation":"used_in_publication","status":"public","id":"14077"}]},"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12933","year":"2023","abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"file_date_updated":"2023-05-11T12:50:18Z","type":"research_data","date_published":"2023-05-15T00:00:00Z","doi":"10.15479/AT:ISTA:12933","citation":{"ieee":"G. 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Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.","short":"G. Puixeu Sala, (2023).","mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933."},"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,"article_processing_charge":"No","has_accepted_license":"1","month":"05","day":"15"},{"quality_controlled":"1","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"},"external_id":{"arxiv":["1612.08215"],"isi":["001047690500001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.2140/pjm.2023.324.265","publication_identifier":{"issn":["0030-8730"],"eissn":["1945-5844"]},"month":"07","department":[{"_id":"TiBr"}],"publisher":"Mathematical Sciences Publishers","publication_status":"published","year":"2023","acknowledgement":"The authors thank the referee for important comments which led to significant improvements is the presentation of several results in the paper. They also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15.","volume":324,"date_created":"2023-08-27T22:01:18Z","date_updated":"2023-12-13T12:19:42Z","author":[{"id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","last_name":"Horesh","first_name":"Tal","full_name":"Horesh, Tal"},{"full_name":"Nevo, Amos","last_name":"Nevo","first_name":"Amos"}],"file_date_updated":"2023-09-05T07:26:17Z","page":"265-294","article_type":"original","citation":{"ista":"Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 324(2), 265–294.","apa":"Horesh, T., & Nevo, A. (2023). Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.324.265","ieee":"T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution,” Pacific Journal of Mathematics, vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.","ama":"Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 2023;324(2):265-294. doi:10.2140/pjm.2023.324.265","chicago":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.324.265.","mla":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp. 265–94, doi:10.2140/pjm.2023.324.265.","short":"T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294."},"publication":"Pacific Journal of Mathematics","date_published":"2023-07-26T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"26","intvolume":" 324","title":"Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution","status":"public","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14245","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":654895,"creator":"dernst","file_name":"2023_PacificJourMaths_Horesh.pdf","access_level":"open_access","date_created":"2023-09-05T07:26:17Z","date_updated":"2023-09-05T07:26:17Z","checksum":"a675b53cfb31fa46be1e879b7e77fe8c","success":1,"relation":"main_file","file_id":"14267"}],"type":"journal_article","issue":"2","abstract":[{"text":"We establish effective counting results for lattice points in families of domains in real, complex and quaternionic hyperbolic spaces of any dimension. The domains we focus on are defined as product sets with respect to an Iwasawa decomposition. Several natural diophantine problems can be reduced to counting lattice points in such domains. These include equidistribution of the ratio of the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose radius increases, the natural analog of this problem in imaginary quadratic number fields, as well as equidistribution of integral solutions to the diophantine equation defined by an integral Lorentz form in three or more variables. We establish an effective rate of convergence for these equidistribution problems, depending on the size of the spectral gap associated with a suitable lattice subgroup in the isometry group of the relevant hyperbolic space. The main result underlying our discussion amounts to establishing effective joint equidistribution for the horospherical component and the radial component in the Iwasawa decomposition of lattice elements.","lang":"eng"}]},{"article_number":"224","file_date_updated":"2023-09-05T08:45:49Z","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt.","year":"2023","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"first_name":"Hans-Werner","last_name":"Hammer","full_name":"Hammer, Hans-Werner"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"volume":6,"date_updated":"2023-12-13T12:21:09Z","date_created":"2023-08-28T12:36:49Z","publication_identifier":{"issn":["2399-3650"]},"month":"08","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"},"external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s42005-023-01281-2","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium."}],"_id":"14246","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","status":"public","title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","ddc":["530"],"file":[{"file_name":"2023_CommPhysics_Brauneis.pdf","access_level":"open_access","file_size":855960,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14268","date_updated":"2023-09-05T08:45:49Z","date_created":"2023-09-05T08:45:49Z","checksum":"6edfc59b0ee7dc406d0968b05236e83d","success":1}],"oa_version":"Published Version","scopus_import":"1","keyword":["General Physics and Astronomy"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"22","citation":{"short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023).","mla":"Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics, vol. 6, 224, Springer Nature, 2023, doi:10.1038/s42005-023-01281-2.","chicago":"Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics. Springer Nature, 2023. https://doi.org/10.1038/s42005-023-01281-2.","ama":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 2023;6. doi:10.1038/s42005-023-01281-2","ieee":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” Communications Physics, vol. 6. Springer Nature, 2023.","apa":"Brauneis, F., Ghazaryan, A., Hammer, H.-W., & Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-023-01281-2","ista":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224."},"publication":"Communications Physics","article_type":"original","date_published":"2023-08-22T00:00:00Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Given a resolution of rational singularities π:X~→X over a field of characteristic zero, we use a Hodge-theoretic argument to prove that the image of the functor Rπ∗:Db(X~)→Db(X)\r\n between bounded derived categories of coherent sheaves generates Db(X)\r\n as a triangulated category. This gives a weak version of the Bondal–Orlov localization conjecture [BO02], answering a question from [PS21]. The same result is established more generally for proper (not necessarily birational) morphisms π:X~→X , with X~\r\n smooth, satisfying Rπ∗(OX~)=OX ."}],"title":"Homological Bondal-Orlov localization conjecture for rational singularities","status":"public","ddc":["510"],"intvolume":" 11","_id":"14239","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2023_ForumMathematics_Mauri.pdf","content_type":"application/pdf","file_size":280865,"creator":"dernst","relation":"main_file","file_id":"14266","checksum":"c36241750cc5cb06890aec0ecdfee626","success":1,"date_created":"2023-09-05T06:43:11Z","date_updated":"2023-09-05T06:43:11Z"}],"oa_version":"Published Version","scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Forum of Mathematics, Sigma","citation":{"chicago":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.65.","mla":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma, vol. 11, e66, Cambridge University Press, 2023, doi:10.1017/fms.2023.65.","short":"M. Mauri, E. Shinder, Forum of Mathematics, Sigma 11 (2023).","ista":"Mauri M, Shinder E. 2023. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 11, e66.","apa":"Mauri, M., & Shinder, E. (2023). Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.65","ieee":"M. Mauri and E. Shinder, “Homological Bondal-Orlov localization conjecture for rational singularities,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023.","ama":"Mauri M, Shinder E. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.65"},"date_published":"2023-08-03T00:00:00Z","article_number":"e66","file_date_updated":"2023-09-05T06:43:11Z","ec_funded":1,"publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Cambridge University Press","year":"2023","acknowledgement":"We thank Agnieszka Bodzenta-Skibińska, Paolo Cascini, Wahei Hara, Sándor Kovács, Alexander Kuznetsov, Mircea Musta ă, Nebojsa Pavic, Pavel Sechin, and Michael Wemyss for discussions and e-mail correspondence. We also thank the anonymous referee for the helpful comments. M.M. was supported by the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 101034413. E.S. was partially supported by the EPSRC grant EP/T019379/1 “Derived categories and algebraic K-theory of singularities”, and by the ERC Synergy grant “Modern Aspects of Geometry: Categories, Cycles and Cohomology of Hyperkähler Varieties.”\r\n\r\n","date_updated":"2023-12-13T12:18:18Z","date_created":"2023-08-27T22:01:16Z","volume":11,"author":[{"full_name":"Mauri, Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","last_name":"Mauri","first_name":"Mirko"},{"last_name":"Shinder","first_name":"Evgeny","full_name":"Shinder, Evgeny"}],"month":"08","publication_identifier":{"eissn":["2050-5094"]},"quality_controlled":"1","isi":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"external_id":{"isi":["001041926700001"],"arxiv":["2212.06786"]},"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,"language":[{"iso":"eng"}],"doi":"10.1017/fms.2023.65"},{"publication_identifier":{"eissn":["1572-9656"],"issn":["1385-0172"]},"month":"07","doi":"10.1007/s11040-023-09460-x","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"},"external_id":{"arxiv":["2206.14708"],"isi":["001032992600001"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2023-08-23T10:59:15Z","article_number":"17","author":[{"full_name":"Lampart, Jonas","first_name":"Jonas","last_name":"Lampart"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"},{"last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof"}],"volume":26,"date_updated":"2023-12-13T12:16:19Z","date_created":"2023-08-22T14:09:47Z","acknowledgement":"D.M. and K.M. thank Robert Seiringer for helpful discussions. Open access funding provided by Institute of Science and Technology (IST Austria). Financial support from the Agence Nationale de la Recherche (ANR) through the projects ANR-17-CE40-0016, ANR-17-CE40-0007-01, ANR-17-EURE-0002 (J.L.) and from the European Union’s Horizon 2020 research and innovation programme under the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.) is gratefully acknowledged.","year":"2023","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"26","scopus_import":"1","keyword":["Geometry and Topology","Mathematical Physics"],"date_published":"2023-07-26T00:00:00Z","citation":{"ista":"Lampart J, Mitrouskas DJ, Mysliwy K. 2023. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 26(3), 17.","apa":"Lampart, J., Mitrouskas, D. J., & Mysliwy, K. (2023). On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. Springer Nature. https://doi.org/10.1007/s11040-023-09460-x","ieee":"J. Lampart, D. J. Mitrouskas, and K. Mysliwy, “On the global minimum of the energy–momentum relation for the polaron,” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3. Springer Nature, 2023.","ama":"Lampart J, Mitrouskas DJ, Mysliwy K. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 2023;26(3). doi:10.1007/s11040-023-09460-x","chicago":"Lampart, Jonas, David Johannes Mitrouskas, and Krzysztof Mysliwy. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry. Springer Nature, 2023. https://doi.org/10.1007/s11040-023-09460-x.","mla":"Lampart, Jonas, et al. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3, 17, Springer Nature, 2023, doi:10.1007/s11040-023-09460-x.","short":"J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023)."},"publication":"Mathematical Physics, Analysis and Geometry","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"For the Fröhlich model of the large polaron, we prove that the ground state energy as a function of the total momentum has a unique global minimum at momentum zero. This implies the non-existence of a ground state of the translation invariant Fröhlich Hamiltonian and thus excludes the possibility of a localization transition at finite coupling."}],"type":"journal_article","file":[{"file_id":"14225","relation":"main_file","date_created":"2023-08-23T10:59:15Z","date_updated":"2023-08-23T10:59:15Z","success":1,"checksum":"f0941cc66cb3ed06a12ca4b7e356cfd6","file_name":"2023_MathPhysics_Lampart.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":317026}],"oa_version":"Published Version","_id":"14192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 26","title":"On the global minimum of the energy–momentum relation for the polaron","ddc":["510"],"status":"public"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We demonstrate that a sodium dimer, Na2(13Σ+u), residing on the surface of a helium nanodroplet, can be set into rotation by a nonresonant 1.0 ps infrared laser pulse. The time-dependent degree of alignment measured, exhibits a periodic, gradually decreasing structure that deviates qualitatively from that expected for gas-phase dimers. Comparison to alignment dynamics calculated from the time-dependent rotational Schrödinger equation shows that the deviation is due to the alignment dependent interaction between the dimer and the droplet surface. This interaction confines the dimer to the tangential plane of the droplet surface at the point where it resides and is the reason that the observed alignment dynamics is also well described by a 2D quantum rotor model."}],"issue":"5","_id":"14238","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Nonadiabatic laser-induced alignment dynamics of molecules on a surface","intvolume":" 131","oa_version":"Preprint","scopus_import":"1","day":"04","article_processing_charge":"No","publication":"Physical Review Letters","citation":{"short":"L. Kranabetter, H.H. Kristensen, A. Ghazaryan, C.A. Schouder, A.S. Chatterley, P. Janssen, F. Jensen, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 131 (2023).","mla":"Kranabetter, Lorenz, et al. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters, vol. 131, no. 5, 053201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.053201.","chicago":"Kranabetter, Lorenz, Henrik H. Kristensen, Areg Ghazaryan, Constant A. Schouder, Adam S. Chatterley, Paul Janssen, Frank Jensen, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.053201.","ama":"Kranabetter L, Kristensen HH, Ghazaryan A, et al. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 2023;131(5). doi:10.1103/PhysRevLett.131.053201","apa":"Kranabetter, L., Kristensen, H. H., Ghazaryan, A., Schouder, C. A., Chatterley, A. S., Janssen, P., … Stapelfeldt, H. (2023). Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.053201","ieee":"L. Kranabetter et al., “Nonadiabatic laser-induced alignment dynamics of molecules on a surface,” Physical Review Letters, vol. 131, no. 5. American Physical Society, 2023.","ista":"Kranabetter L, Kristensen HH, Ghazaryan A, Schouder CA, Chatterley AS, Janssen P, Jensen F, Zillich RE, Lemeshko M, Stapelfeldt H. 2023. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 131(5), 053201."},"article_type":"original","date_published":"2023-08-04T00:00:00Z","article_number":"053201","ec_funded":1,"acknowledgement":"H. S. acknowledges support from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). F. J. and R. E. Z. acknowledge support from the Centre for Scientific Computing, Aarhus and the JKU scientific computing administration, Linz, respectively.","year":"2023","pmid":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"author":[{"full_name":"Kranabetter, Lorenz","first_name":"Lorenz","last_name":"Kranabetter"},{"full_name":"Kristensen, Henrik H.","first_name":"Henrik H.","last_name":"Kristensen"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"last_name":"Schouder","first_name":"Constant A.","full_name":"Schouder, Constant A."},{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"last_name":"Janssen","first_name":"Paul","full_name":"Janssen, Paul"},{"full_name":"Jensen, Frank","first_name":"Frank","last_name":"Jensen"},{"last_name":"Zillich","first_name":"Robert E.","full_name":"Zillich, Robert E."},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt","first_name":"Henrik"}],"date_created":"2023-08-27T22:01:16Z","date_updated":"2023-12-13T12:18:54Z","volume":131,"month":"08","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2308.15247","open_access":"1"}],"external_id":{"arxiv":["2308.15247"],"pmid":["37595218"],"isi":["001101784100001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"doi":"10.1103/PhysRevLett.131.053201","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"month":"08","oa":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"},"external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1371/journal.ppat.1011562","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"article_number":"e1011562","file_date_updated":"2023-09-06T06:41:52Z","pmid":1,"year":"2023","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","department":[{"_id":"FlSc"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"first_name":"Jana","last_name":"Koch","full_name":"Koch, Jana"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"full_name":"Obr, Martin","last_name":"Obr","first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alicia","last_name":"Schäfer","full_name":"Schäfer, Alicia"},{"full_name":"Rolfs, Nina","first_name":"Nina","last_name":"Rolfs"},{"last_name":"Anagho","first_name":"Holda A.","full_name":"Anagho, Holda A."},{"last_name":"Kudulyte","first_name":"Aiste","full_name":"Kudulyte, Aiste"},{"last_name":"Woltereck","first_name":"Lea","full_name":"Woltereck, Lea"},{"last_name":"Kummer","first_name":"Susann","full_name":"Kummer, Susann"},{"first_name":"Joaquin","last_name":"Campos","full_name":"Campos, Joaquin"},{"last_name":"Uckeley","first_name":"Zina M.","full_name":"Uckeley, Zina M."},{"last_name":"Bell-Sakyi","first_name":"Lesley","full_name":"Bell-Sakyi, Lesley"},{"last_name":"Kräusslich","first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","last_name":"Schur","full_name":"Schur, Florian Km"},{"full_name":"Acuna, Claudio","first_name":"Claudio","last_name":"Acuna"},{"last_name":"Lozach","first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves"}],"volume":19,"date_created":"2023-09-03T22:01:14Z","date_updated":"2023-12-13T12:22:22Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"14","citation":{"short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562.","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens. Public Library of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562.","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8). doi:10.1371/journal.ppat.1011562","ieee":"J. Koch et al., “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no. 8. Public Library of Science, 2023.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1011562","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562."},"publication":"PLoS Pathogens","article_type":"original","date_published":"2023-08-14T00:00:00Z","type":"journal_article","issue":"8","abstract":[{"text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14255","intvolume":" 19","status":"public","ddc":["570"],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","oa_version":"Published Version","file":[{"date_created":"2023-09-06T06:41:52Z","date_updated":"2023-09-06T06:41:52Z","success":1,"checksum":"47ca3bb54b27f28b05644be0ad064bc6","file_id":"14269","relation":"main_file","creator":"dernst","file_size":4458336,"content_type":"application/pdf","file_name":"2023_PloSPathogens_Koch.pdf","access_level":"open_access"}]},{"doi":"10.1038/s41477-023-01478-x","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"},"external_id":{"pmid":["37666965"],"isi":["001069238800014"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2055-0278"]},"month":"09","author":[{"first_name":"S","last_name":"Roychoudhry","full_name":"Roychoudhry, S"},{"full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas","first_name":"K"},{"last_name":"Wolverton","first_name":"C","full_name":"Wolverton, C"},{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"last_name":"De Angelis","first_name":"M","full_name":"De Angelis, M"},{"full_name":"Goodman, HL","first_name":"HL","last_name":"Goodman"},{"full_name":"Capstaff, N","last_name":"Capstaff","first_name":"N"},{"full_name":"JPB, Lloyd","last_name":"JPB","first_name":"Lloyd"},{"full_name":"Mullen, J","first_name":"J","last_name":"Mullen"},{"first_name":"R","last_name":"Hangarter","full_name":"Hangarter, R"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Kepinski","first_name":"S","full_name":"Kepinski, S"}],"volume":9,"date_updated":"2023-12-13T12:23:49Z","date_created":"2023-09-15T09:56:01Z","pmid":1,"year":"2023","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2023-09-20T10:51:31Z","date_published":"2023-09-01T00:00:00Z","citation":{"chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature, 2023. https://doi.org/10.1038/s41477-023-01478-x.","mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:10.1038/s41477-023-01478-x.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x","ieee":"S. Roychoudhry et al., “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer Nature, pp. 1500–1513, 2023.","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513. doi:10.1038/s41477-023-01478-x"},"publication":"Nature Plants","page":"1500-1513","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","file":[{"date_created":"2023-09-20T10:51:31Z","date_updated":"2023-09-20T10:51:31Z","success":1,"checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","file_id":"14351","relation":"main_file","creator":"dernst","file_size":9647103,"content_type":"application/pdf","file_name":"2023_NaturePlants_Roychoudhry.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"14339","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","status":"public","ddc":["580"],"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","abstract":[{"text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.","lang":"eng"}],"type":"journal_article"},{"publication":"iScience","citation":{"ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780","ieee":"M. E. Maes et al., “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” iScience, vol. 26, no. 10. Elsevier, 2023.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780.","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience, vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023)."},"article_type":"original","date_published":"2023-10-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"Yes","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14363","ddc":["570"],"title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","status":"public","intvolume":" 26","file":[{"access_level":"open_access","file_name":"2023_iScience_Maes.pdf","file_size":8197935,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14497","checksum":"be1a560efdd96d20712311f4fc54aac2","success":1,"date_created":"2023-11-07T08:53:21Z","date_updated":"2023-11-07T08:53:21Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies."}],"issue":"10","oa":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"},"external_id":{"isi":["001080403500001"],"pmid":["37731609"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.isci.2023.107780","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2589-0042"]},"acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","year":"2023","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SaSi"}],"author":[{"first_name":"Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","first_name":"Gloria","last_name":"Colombo","full_name":"Colombo, Gloria"},{"full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"full_name":"Sternberg, Felix","last_name":"Sternberg","first_name":"Felix"},{"orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro"},{"last_name":"Pohl","first_name":"Elena E.","full_name":"Pohl, Elena E."},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"date_created":"2023-09-24T22:01:11Z","date_updated":"2023-12-13T12:27:30Z","volume":26,"article_number":"107780","file_date_updated":"2023-11-07T08:53:21Z"},{"volume":11,"date_updated":"2023-12-13T12:24:23Z","date_created":"2023-09-17T22:01:09Z","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","last_name":"Henheik","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha"},{"id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61","first_name":"Oleksii","last_name":"Kolupaiev","full_name":"Kolupaiev, Oleksii"}],"department":[{"_id":"LaEr"},{"_id":"GradSch"}],"publisher":"Cambridge University Press","publication_status":"published","acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","year":"2023","ec_funded":1,"file_date_updated":"2023-09-20T11:09:35Z","article_number":"e74","language":[{"iso":"eng"}],"doi":"10.1017/fms.2023.70","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"quality_controlled":"1","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"},"external_id":{"arxiv":["2301.05181"],"isi":["001051980200001"]},"oa":1,"publication_identifier":{"eissn":["2050-5094"]},"month":"08","file":[{"creator":"dernst","file_size":852652,"content_type":"application/pdf","file_name":"2023_ForumMathematics_Cipolloni.pdf","access_level":"open_access","date_updated":"2023-09-20T11:09:35Z","date_created":"2023-09-20T11:09:35Z","success":1,"checksum":"eb747420e6a88a7796fa934151957676","file_id":"14352","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 11","ddc":["510"],"status":"public","title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","_id":"14343","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation."}],"type":"journal_article","date_published":"2023-08-23T00:00:00Z","article_type":"original","citation":{"short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge University Press, 2023, doi:10.1017/fms.2023.70.","chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70.","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.70","ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023.","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70","ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74."},"publication":"Forum of Mathematics, Sigma","has_accepted_license":"1","article_processing_charge":"Yes","day":"23","scopus_import":"1"},{"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"07","oa":1,"external_id":{"isi":["001082972300004"],"arxiv":["1811.01421"]},"main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1137/20M1375851","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","year":"2023","department":[{"_id":"DaAl"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6676"}]},"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"first_name":"Faith","last_name":"Ellen","full_name":"Ellen, Faith"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","last_name":"Zhu","first_name":"Leqi","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5"}],"volume":52,"date_updated":"2023-12-13T12:28:29Z","date_created":"2023-09-24T22:01:11Z","scopus_import":"1","article_processing_charge":"No","day":"25","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20M1375851.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:10.1137/20M1375851.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2023). Why extension-based proofs fail. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1375851","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” SIAM Journal on Computing, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. SIAM Journal on Computing. 2023;52(4):913-944. doi:10.1137/20M1375851"},"publication":"SIAM Journal on Computing","page":"913-944","article_type":"original","date_published":"2023-07-25T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among processes or approximate agreement on a cycle of length 4 among processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14364","intvolume":" 52","status":"public","title":"Why extension-based proofs fail","oa_version":"Preprint"},{"status":"public","title":"On angles in higher order Brillouin tessellations and related tilings in the plane","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14345","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"For a locally finite set in R2, the order-k Brillouin tessellations form an infinite sequence of convex face-to-face tilings of the plane. If the set is coarsely dense and generic, then the corresponding infinite sequences of minimum and maximum angles are both monotonic in k. As an example, a stationary Poisson point process in R2 is locally finite, coarsely dense, and generic with probability one. For such a set, the distributions of angles in the Voronoi tessellations, Delaunay mosaics, and Brillouin tessellations are independent of the order and can be derived from the formula for angles in order-1 Delaunay mosaics given by Miles (Math. Biosci. 6, 85–127 (1970)).","lang":"eng"}],"article_type":"original","citation":{"short":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023).","mla":"Edelsbrunner, Herbert, et al. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00566-1.","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafari, Teresa Heiss, and Morteza Saghafian. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00566-1.","ama":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00566-1","apa":"Edelsbrunner, H., Garber, A., Ghafari, M., Heiss, T., & Saghafian, M. (2023). On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00566-1","ieee":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, and M. Saghafian, “On angles in higher order Brillouin tessellations and related tilings in the plane,” Discrete and Computational Geometry. Springer Nature, 2023.","ista":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. 2023. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry."},"publication":"Discrete and Computational Geometry","date_published":"2023-09-07T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","day":"07","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"epub_ahead","year":"2023","acknowledgement":"Work by all authors but A. Garber is supported by the European Research Council (ERC), Grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), Grant No. I 02979-N35. Work by A. Garber is partially supported by the Alexander von Humboldt Foundation.","date_updated":"2023-12-13T12:25:06Z","date_created":"2023-09-17T22:01:10Z","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"first_name":"Alexey","last_name":"Garber","full_name":"Garber, Alexey"},{"full_name":"Ghafari, Mohadese","last_name":"Ghafari","first_name":"Mohadese"},{"full_name":"Heiss, Teresa","first_name":"Teresa","last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-023-00566-1","open_access":"1"}],"external_id":{"arxiv":["2204.01076"],"isi":["001060727600004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-023-00566-1","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"09"},{"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"21","article_type":"original","citation":{"mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications, vol. 14, 5878, Springer Nature, 2023, doi:10.1038/s41467-023-41456-7.","short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 2023;14. doi:10.1038/s41467-023-41456-7","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., & Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41456-7","ieee":"M. C. Ucar et al., “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” Nature Communications, vol. 14. Springer Nature, 2023."},"publication":"Nature Communications","date_published":"2023-09-21T00:00:00Z","type":"journal_article","abstract":[{"text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.","lang":"eng"}],"intvolume":" 14","title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","ddc":["570"],"status":"public","_id":"14378","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"4fe5423403f2531753bcd9e0fea48e05","success":1,"date_created":"2023-10-03T07:46:36Z","date_updated":"2023-10-03T07:46:36Z","relation":"main_file","file_id":"14384","file_size":8143264,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_NatureComm_Ucar.pdf"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"month":"09","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"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"},"external_id":{"isi":["001075884500007"],"pmid":["37735168"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-41456-7","article_number":"5878","ec_funded":1,"file_date_updated":"2023-10-03T07:46:36Z","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","volume":14,"date_updated":"2023-12-13T12:31:05Z","date_created":"2023-10-01T22:01:13Z","author":[{"full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Tiilikainen","first_name":"Emmi","full_name":"Tiilikainen, Emmi"},{"first_name":"Inam","last_name":"Liaqat","full_name":"Liaqat, Inam"},{"full_name":"Jakobsson, Emma","last_name":"Jakobsson","first_name":"Emma"},{"first_name":"Harri","last_name":"Nurmi","full_name":"Nurmi, Harri"},{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari"}]},{"file_date_updated":"2023-09-25T08:32:37Z","ec_funded":1,"article_number":"5633","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael"},{"full_name":"Mayer, Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","last_name":"Mayer"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"date_created":"2023-09-24T22:01:10Z","date_updated":"2023-12-13T12:29:41Z","volume":14,"acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"publisher":"Springer Nature","month":"09","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-41432-1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"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,"isi":1,"quality_controlled":"1","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Riedl.pdf","content_type":"application/pdf","file_size":2317272,"creator":"dernst","relation":"main_file","file_id":"14366","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","success":1,"date_updated":"2023-09-25T08:32:37Z","date_created":"2023-09-25T08:32:37Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14361","status":"public","ddc":["530","570"],"title":"Synchronization in collectively moving inanimate and living active matter","intvolume":" 14","day":"13","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-09-13T00:00:00Z","publication":"Nature Communications","citation":{"ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1."},"article_type":"original"},{"type":"journal_article","issue":"44","abstract":[{"text":"Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\\in\\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission).","lang":"eng"}],"_id":"14421","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 56","status":"public","ddc":["510"],"title":"Creation rate of Dirac particles at a point source","file":[{"creator":"dernst","file_size":721399,"content_type":"application/pdf","file_name":"2023_JourPhysics_Henheik.pdf","access_level":"open_access","date_created":"2023-10-16T07:07:24Z","date_updated":"2023-10-16T07:07:24Z","success":1,"checksum":"5b68de147dd4c608b71a6e0e844d2ce9","file_id":"14429","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"11","citation":{"apa":"Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62","ieee":"S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44. IOP Publishing, 2023.","ista":"Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.","ama":"Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62","chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.","short":"S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62."},"publication":"Journal of Physics A: Mathematical and Theoretical","article_type":"original","date_published":"2023-10-11T00:00:00Z","article_number":"445201","ec_funded":1,"file_date_updated":"2023-10-16T07:07:24Z","year":"2023","acknowledgement":"J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331.","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"publisher":"IOP Publishing","publication_status":"published","author":[{"full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X"},{"last_name":"Tumulka","first_name":"Roderich","full_name":"Tumulka, Roderich"}],"volume":56,"date_created":"2023-10-12T12:42:53Z","date_updated":"2023-12-13T13:01:25Z","publication_identifier":{"issn":["1751-8113"],"eissn":["1751-8121"]},"month":"10","external_id":{"isi":["001080908000001"],"arxiv":["2211.16606"]},"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,"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"isi":1,"quality_controlled":"1","doi":"10.1088/1751-8121/acfe62","language":[{"iso":"eng"}]},{"date_published":"2023-09-27T00:00:00Z","publication":"Nonlinear Analysis: Hybrid Systems","citation":{"chicago":"Majumdar, Rupak, Kaushik Mallik, Anne Kathrin Schmuck, and Sadegh Soudjani. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2023. https://doi.org/10.1016/j.nahs.2023.101430.","short":"R. Majumdar, K. Mallik, A.K. Schmuck, S. Soudjani, Nonlinear Analysis: Hybrid Systems 51 (2023).","mla":"Majumdar, Rupak, et al. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems, vol. 51, 101430, Elsevier, 2023, doi:10.1016/j.nahs.2023.101430.","apa":"Majumdar, R., Mallik, K., Schmuck, A. K., & Soudjani, S. (2023). Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2023.101430","ieee":"R. Majumdar, K. Mallik, A. K. Schmuck, and S. Soudjani, “Symbolic control for stochastic systems via finite parity games,” Nonlinear Analysis: Hybrid Systems, vol. 51. Elsevier, 2023.","ista":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. 2023. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 51, 101430.","ama":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 2023;51. doi:10.1016/j.nahs.2023.101430"},"article_type":"original","day":"27","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14400","status":"public","title":"Symbolic control for stochastic systems via finite parity games","intvolume":" 51","abstract":[{"lang":"eng","text":"We consider the problem of computing the maximal probability of satisfying an \r\n-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.\r\nThe heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a \r\n-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve \r\n-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.\r\nWe have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves \r\n-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin."}],"type":"journal_article","doi":"10.1016/j.nahs.2023.101430","language":[{"iso":"eng"}],"external_id":{"isi":["001093188100001"],"arxiv":["2101.00834"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.nahs.2023.101430","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"month":"09","publication_identifier":{"issn":["1751-570X"]},"author":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"full_name":"Mallik, Kaushik","first_name":"Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475"},{"last_name":"Schmuck","first_name":"Anne Kathrin","full_name":"Schmuck, Anne Kathrin"},{"last_name":"Soudjani","first_name":"Sadegh","full_name":"Soudjani, Sadegh"}],"date_created":"2023-10-08T22:01:15Z","date_updated":"2023-12-13T12:58:56Z","volume":51,"acknowledgement":"We thank Daniel Hausmann and Nir Piterman for their valuable comments on an earlier version of the manuscript of our other paper [22] where we present, among other things, the parity fixpoint for 2 1/2-player games (for a slightly more general class of games) with a different and indirect proof of correctness. Based on their comments we observed that, unlike the other fixpoints that we present in [22], the parity fixpoint does not follow the exact same structure as its counterpart for 2-player games, which we also use int his paper.\r\nWe also thank Thejaswini Raghavan for observing that our symbolic parity fixpoint algorithm can be solved in quasi-polynomial time using recent improved algorithms for solving \r\n-calculus expressions. This significantly improved the complexity bounds of our algorithm in this paper.\r\nThe work of R. Majumdar and A.-K. Schmuck are partially supported by DFG, Germany project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG, Germany project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047.","year":"2023","publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"ToHe"}],"ec_funded":1,"article_number":"101430"},{"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","ddc":["540","000"],"status":"public","intvolume":" 14","_id":"14425","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":3194116,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_NatureComm_Zeng.pdf","checksum":"7d1dffd36b672ec679f08f70ce79da87","success":1,"date_created":"2023-10-16T07:34:49Z","date_updated":"2023-10-16T07:34:49Z","relation":"main_file","file_id":"14432"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces."}],"article_type":"original","publication":"Nature Communications","citation":{"ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131.","apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., & Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41865-8","ieee":"Z. Zeng et al., “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 2023;14. doi:10.1038/s41467-023-41865-8","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41865-8.","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications, vol. 14, 6131, Springer Nature, 2023, doi:10.1038/s41467-023-41865-8.","short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023)."},"date_published":"2023-10-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"Yes","has_accepted_license":"1","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","year":"2023","pmid":1,"date_created":"2023-10-15T22:01:10Z","date_updated":"2023-12-13T13:02:07Z","volume":14,"author":[{"first_name":"Zezhu","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","full_name":"Zeng, Zezhu"},{"first_name":"Felix","last_name":"Wodaczek","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","orcid":"0009-0000-1457-795X","full_name":"Wodaczek, Felix"},{"full_name":"Liu, Keyang","last_name":"Liu","first_name":"Keyang"},{"full_name":"Stein, Frederick","first_name":"Frederick","last_name":"Stein"},{"first_name":"Jürg","last_name":"Hutter","full_name":"Hutter, Jürg"},{"full_name":"Chen, Ji","first_name":"Ji","last_name":"Chen"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"}],"related_material":{"link":[{"url":"https://github.com/BingqingCheng/TiO2-water","relation":"software"}]},"article_number":"6131","file_date_updated":"2023-10-16T07:34:49Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"external_id":{"pmid":["37783698"],"isi":["001084354900008"],"arxiv":["2303.07433"]},"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,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-41865-8","month":"10","publication_identifier":{"eissn":["2041-1723"]}},{"type":"journal_article","issue":"10","abstract":[{"text":"Squall lines are substantially influenced by the interaction of low-level shear with cold pools associated with convective downdrafts. Beyond an optimal shear amplitude, squall lines tend to orient themselves at an angle with respect to the low-level shear. While the mechanisms behind squall line orientation seem to be increasingly well understood, uncertainties remain on the implications of this orientation. Roca and Fiolleau (2020, https://doi.org/10.1038/s43247-020-00015-4) show that long lived mesoscale convective systems, including squall lines, are disproportionately involved in rainfall extremes in the tropics. This article investigates the influence of the interaction between low-level shear and squall line outflow on squall line generated precipitation extrema in the tropics. Using a cloud resolving model, simulated squall lines in radiative convective equilibrium amid a shear-dominated regime (super optimal), a balanced regime (optimal), and an outflow dominated regime (suboptimal). Our results show that precipitation extremes in squall lines are 40% more intense in the case of optimal shear and remain 30% superior in the superoptimal regime relative to a disorganized case. With a theoretical scaling of precipitation extremes (C. Muller & Takayabu, 2020, https://doi.org/10.1088/1748-9326/ab7130), we show that the condensation rates control the amplification of precipitation extremes in tropical squall lines, mainly due to its change in vertical mass flux (dynamic component). The reduction of dilution by entrainment explains half of this change, consistent with Mulholland et al. (2021, https://doi.org/10.1175/jas-d-20-0299.1). The other half is explained by increased cloud-base velocity intensity in optimal and superoptimal squall lines.","lang":"eng"}],"intvolume":" 15","status":"public","ddc":["550"],"title":"Extreme precipitation in tropical squall lines","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14453","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_JAMES_Abramian.pdf","content_type":"application/pdf","file_size":1975210,"creator":"dernst","relation":"main_file","file_id":"14470","checksum":"43e6a1a35b663843c7d3f8d0caaca1a5","success":1,"date_created":"2023-10-30T13:31:42Z","date_updated":"2023-10-30T13:31:42Z"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","article_type":"original","citation":{"chicago":"Abramian, Sophie, Caroline J Muller, and Camille Risi. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems. Wiley, 2023. https://doi.org/10.1029/2022MS003477.","mla":"Abramian, Sophie, et al. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10, e2022MS003477, Wiley, 2023, doi:10.1029/2022MS003477.","short":"S. Abramian, C.J. Muller, C. Risi, Journal of Advances in Modeling Earth Systems 15 (2023).","ista":"Abramian S, Muller CJ, Risi C. 2023. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 15(10), e2022MS003477.","ieee":"S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical squall lines,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10. Wiley, 2023.","apa":"Abramian, S., Muller, C. J., & Risi, C. (2023). Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2022MS003477","ama":"Abramian S, Muller CJ, Risi C. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 2023;15(10). doi:10.1029/2022MS003477"},"publication":"Journal of Advances in Modeling Earth Systems","date_published":"2023-10-01T00:00:00Z","article_number":"e2022MS003477","ec_funded":1,"file_date_updated":"2023-10-30T13:31:42Z","department":[{"_id":"CaMu"}],"publisher":"Wiley","publication_status":"published","year":"2023","acknowledgement":"The authors gratefully acknowledge funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This work is also supported by a PhD fellowship funded by the Ecole Normale Supérieure de Paris-Saclay. Authors are also grateful to Benjamin Filider, who was of great help and support in the development of ideas. Eventually, we would like to thank Martin Singh, John M. Peters and an anonymous reviewer for their valuable comments and suggestions, which greatly improved the quality of the manuscript.","volume":15,"date_created":"2023-10-29T23:01:15Z","date_updated":"2023-12-13T13:06:40Z","author":[{"first_name":"Sophie","last_name":"Abramian","full_name":"Abramian, Sophie"},{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J","last_name":"Muller"},{"first_name":"Camille","last_name":"Risi","full_name":"Risi, Camille"}],"publication_identifier":{"eissn":["1942-2466"]},"month":"10","project":[{"call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"quality_controlled":"1","isi":1,"oa":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"},"external_id":{"isi":["001084933600001"]},"language":[{"iso":"eng"}],"doi":"10.1029/2022MS003477"},{"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"day":"24","article_processing_charge":"No","article_type":"original","publication":"Advanced Materials","citation":{"short":"R. He, L. Yang, Y. Zhang, D. Jiang, S. Lee, S. Horta, Z. Liang, X. Lu, A. Ostovari Moghaddam, J. Li, M. Ibáñez, Y. Xu, Y. Zhou, A. Cabot, Advanced Materials (2023).","mla":"He, Ren, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials, 2303719, Wiley, 2023, doi:10.1002/adma.202303719.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Daochuan Jiang, Seungho Lee, Sharona Horta, Zhifu Liang, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202303719.","ama":"He R, Yang L, Zhang Y, et al. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. 2023. doi:10.1002/adma.202303719","ieee":"R. He et al., “A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries,” Advanced Materials. Wiley, 2023.","apa":"He, R., Yang, L., Zhang, Y., Jiang, D., Lee, S., Horta, S., … Cabot, A. (2023). A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202303719","ista":"He R, Yang L, Zhang Y, Jiang D, Lee S, Horta S, Liang Z, Lu X, Ostovari Moghaddam A, Li J, Ibáñez M, Xu Y, Zhou Y, Cabot A. 2023. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials., 2303719."},"date_published":"2023-07-24T00:00:00Z","type":"journal_article","abstract":[{"text":"High entropy alloys (HEAs) are highly suitable candidate catalysts for oxygen evolution and reduction reactions (OER/ORR) as they offer numerous parameters for optimizing the electronic structure and catalytic sites. Herein, FeCoNiMoW HEA nanoparticles are synthesized using a solution‐based low‐temperature approach. Such FeCoNiMoW nanoparticles show high entropy properties, subtle lattice distortions, and modulated electronic structure, leading to superior OER performance with an overpotential of 233 mV at 10 mA cm−2 and 276 mV at 100 mA cm−2. Density functional theory calculations reveal the electronic structures of the FeCoNiMoW active sites with an optimized d‐band center position that enables suitable adsorption of OOH* intermediates and reduces the Gibbs free energy barrier in the OER process. Aqueous zinc–air batteries (ZABs) based on this HEA demonstrate a high open circuit potential of 1.59 V, a peak power density of 116.9 mW cm−2, a specific capacity of 857 mAh gZn−1, and excellent stability for over 660 h of continuous charge–discharge cycles. Flexible and solid ZABs are also assembled and tested, displaying excellent charge–discharge performance at different bending angles. This work shows the significance of 4d/5d metal‐modulated electronic structure and optimized adsorption ability to improve the performance of OER/ORR, ZABs, and beyond.","lang":"eng"}],"title":"A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries","status":"public","_id":"14434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"07","publication_identifier":{"issn":["0935-9648","1521-4095"]},"isi":1,"quality_controlled":"1","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"external_id":{"pmid":["37487245"],"isi":["001083876900001"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1002/adma.202303719","article_number":"2303719","publication_status":"epub_ahead","publisher":"Wiley","department":[{"_id":"MaIb"}],"acknowledgement":"The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581; the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación; the National Natural Science Foundation of China (22102002); the Anhui Provincial Natural Science Foundation (2108085QE192); Zhejiang Province key research and development project (2023C01191); the Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering (GrantNo.2022-K31); and The Key Research and Development Program of Hebei Province (20314305D). IREC is funded by the CERCA Programme from the Generalitat de Catalunya. L.L.Y. thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This research was supported by the Scientific Service Units (SSU) of ISTA (Institute of Science and Technology Austria) through resources provided by the Electron Microscopy Facility (EMF). S.L., S.H., and M.I. acknowledge funding by ISTA and the Werner Siemens.","year":"2023","pmid":1,"date_created":"2023-10-17T10:52:23Z","date_updated":"2023-12-13T13:03:23Z","author":[{"full_name":"He, Ren","first_name":"Ren","last_name":"He"},{"last_name":"Yang","first_name":"Linlin","full_name":"Yang, Linlin"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"full_name":"Jiang, Daochuan","first_name":"Daochuan","last_name":"Jiang"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona"},{"full_name":"Liang, Zhifu","last_name":"Liang","first_name":"Zhifu"},{"first_name":"Xuan","last_name":"Lu","full_name":"Lu, Xuan"},{"full_name":"Ostovari Moghaddam, Ahmad","last_name":"Ostovari Moghaddam","first_name":"Ahmad"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"first_name":"Ying","last_name":"Xu","full_name":"Xu, Ying"},{"full_name":"Zhou, Yingtang","first_name":"Yingtang","last_name":"Zhou"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}]},{"publication":"Advanced Materials","citation":{"chicago":"Zeng, Guifang, Qing Sun, Sharona Horta, Shang Wang, Xuan Lu, Chaoyue Zhang, Jing Li, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials. Wiley, n.d. https://doi.org/10.1002/adma.202305128.","short":"G. Zeng, Q. Sun, S. Horta, S. Wang, X. Lu, C. Zhang, J. Li, J. Li, L. Ci, Y. Tian, M. Ibáñez, A. Cabot, Advanced Materials (n.d.).","mla":"Zeng, Guifang, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials, 2305128, Wiley, doi:10.1002/adma.202305128.","apa":"Zeng, G., Sun, Q., Horta, S., Wang, S., Lu, X., Zhang, C., … Cabot, A. (n.d.). A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202305128","ieee":"G. Zeng et al., “A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries,” Advanced Materials. Wiley.","ista":"Zeng G, Sun Q, Horta S, Wang S, Lu X, Zhang C, Li J, Li J, Ci L, Tian Y, Ibáñez M, Cabot A. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials., 2305128.","ama":"Zeng G, Sun Q, Horta S, et al. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. doi:10.1002/adma.202305128"},"external_id":{"isi":["001085681000001"],"pmid":["37555532"]},"quality_controlled":"1","isi":1,"article_type":"original","date_published":"2023-08-09T00:00:00Z","doi":"10.1002/adma.202305128","language":[{"iso":"eng"}],"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"month":"08","day":"09","article_processing_charge":"No","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"_id":"14435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","pmid":1,"status":"public","publication_status":"accepted","title":"A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries","department":[{"_id":"MaIb"}],"publisher":"Wiley","author":[{"full_name":"Zeng, Guifang","first_name":"Guifang","last_name":"Zeng"},{"full_name":"Sun, Qing","first_name":"Qing","last_name":"Sun"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona"},{"full_name":"Wang, Shang","first_name":"Shang","last_name":"Wang"},{"first_name":"Xuan","last_name":"Lu","full_name":"Lu, Xuan"},{"first_name":"Chaoyue","last_name":"Zhang","full_name":"Zhang, Chaoyue"},{"full_name":"Li, Jing","last_name":"Li","first_name":"Jing"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"first_name":"Lijie","last_name":"Ci","full_name":"Ci, Lijie"},{"first_name":"Yanhong","last_name":"Tian","full_name":"Tian, Yanhong"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"date_updated":"2023-12-13T13:03:53Z","date_created":"2023-10-17T10:53:56Z","oa_version":"None","article_number":"2305128","type":"journal_article","abstract":[{"text":"Low‐cost, safe, and environmental‐friendly rechargeable aqueous zinc‐ion batteries (ZIBs) are promising as next‐generation energy storage devices for wearable electronics among other applications. However, sluggish ionic transport kinetics and the unstable electrode structure during ionic insertion/extraction hampers their deployment. Herein, we propose a new cathode material based on a layered metal chalcogenide (LMC), bismuth telluride (Bi2Te3), coated with polypyrrole (PPy). Taking advantage of the PPy coating, the Bi2Te3@PPy composite presents strong ionic absorption affinity, high oxidation resistance, and high structural stability. The ZIBs based on Bi2Te3@PPy cathodes exhibit high capacities and ultra‐long lifespans of over 5000 cycles. They also present outstanding stability even under bending. In addition, we analyze here the reaction mechanism using in situ X‐ray diffraction, X‐ray photoelectron spectroscopy, and computational tools and demonstrate that, in the aqueous system, Zn2+ is not inserted into the cathode as previously assumed. In contrast, proton charge storage dominates the process. Overall, this work not only shows the great potential of LMCs as ZIBs cathode materials and the advantages of PPy coating, but also clarifies the charge/discharge mechanism in rechargeable ZIBs based on LMCs.","lang":"eng"}]},{"oa_version":"Published Version","_id":"14463","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","status":"public","abstract":[{"text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.","lang":"eng"}],"type":"journal_article","date_published":"2023-10-16T00:00:00Z","publication":"Molecular Ecology","citation":{"short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160.","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology."},"article_type":"original","day":"16","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","author":[{"full_name":"Reeve, James","first_name":"James","last_name":"Reeve"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"first_name":"Eva L.","last_name":"Koch","full_name":"Koch, Eva L."},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"date_updated":"2023-12-13T13:05:27Z","date_created":"2023-10-29T23:01:17Z","acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","year":"2023","pmid":1,"publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Wiley","doi":"10.1111/mec.17160","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.17160"}],"oa":1,"external_id":{"isi":["001085119000001"],"pmid":["37843465"]},"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]}},{"article_number":"1287879","file_date_updated":"2023-10-30T12:48:40Z","acknowledgement":"The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work has been partially supported by Italian Ministry of Health Grant RC2023 (and the 5 × 1,000 voluntary contributions). The authors thank the children and their families with whom they work daily.","year":"2023","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"GaNo"}],"author":[{"last_name":"Narzisi","first_name":"Antonio","full_name":"Narzisi, Antonio"},{"last_name":"Halladay","first_name":"Alycia","full_name":"Halladay, Alycia"},{"last_name":"Masi","first_name":"Gabriele","full_name":"Masi, Gabriele"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Catherine","last_name":"Lord","full_name":"Lord, Catherine"}],"date_created":"2023-10-29T23:01:16Z","date_updated":"2023-12-13T13:06:07Z","volume":14,"month":"10","publication_identifier":{"eissn":["1664-0640"]},"oa":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"},"external_id":{"isi":["001084841700001"],"pmid":["37854442"]},"isi":1,"quality_controlled":"1","doi":"10.3389/fpsyt.2023.1287879","language":[{"iso":"eng"}],"type":"journal_article","_id":"14455","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment","ddc":["570"],"intvolume":" 14","oa_version":"Published Version","file":[{"file_name":"2023_FrontiersPsychiatry_Narzisi.pdf","access_level":"open_access","creator":"dernst","file_size":147878,"content_type":"application/pdf","file_id":"14468","relation":"main_file","date_updated":"2023-10-30T12:48:40Z","date_created":"2023-10-30T12:48:40Z","success":1,"checksum":"0a76373e9a4c0fc199f80380de257e86"}],"scopus_import":"1","day":"03","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Frontiers in Psychiatry","citation":{"chicago":"Narzisi, Antonio, Alycia Halladay, Gabriele Masi, Gaia Novarino, and Catherine Lord. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry. Frontiers, 2023. https://doi.org/10.3389/fpsyt.2023.1287879.","mla":"Narzisi, Antonio, et al. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry, vol. 14, 1287879, Frontiers, 2023, doi:10.3389/fpsyt.2023.1287879.","short":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, C. Lord, Frontiers in Psychiatry 14 (2023).","ista":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. 2023. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 14, 1287879.","apa":"Narzisi, A., Halladay, A., Masi, G., Novarino, G., & Lord, C. (2023). Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. Frontiers. https://doi.org/10.3389/fpsyt.2023.1287879","ieee":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, and C. Lord, “Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment,” Frontiers in Psychiatry, vol. 14. Frontiers, 2023.","ama":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 2023;14. doi:10.3389/fpsyt.2023.1287879"},"article_type":"letter_note","date_published":"2023-10-03T00:00:00Z"},{"oa":1,"external_id":{"isi":["001073177200001"],"arxiv":["1902.07330"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07330"}],"project":[{"call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00220-023-04837-z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"09","year":"2023","acknowledgement":"VK acknowledges a partial support by the NSF grant DMS-1402164 and ERC Grant #885707. Discussions with Martin Leguil and Jacopo De Simoi were very useful. JC visited the University of Maryland and thanks for the hospitality. Also, JC was partially supported by the National Key Research and Development Program of China (No.2022YFA1005802), the NSFC Grant 12001392 and NSF of Jiangsu BK20200850. H.-K. Zhang is partially supported by the National Science Foundation (DMS-2220211), as well as Simons Foundation Collaboration Grants for Mathematicians (706383).","publisher":"Springer Nature","department":[{"_id":"VaKa"}],"publication_status":"epub_ahead","author":[{"last_name":"Chen","first_name":"Jianyu","full_name":"Chen, Jianyu"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"full_name":"Zhang, Hong Kun","first_name":"Hong Kun","last_name":"Zhang"}],"date_updated":"2023-12-13T13:02:44Z","date_created":"2023-10-15T22:01:11Z","ec_funded":1,"citation":{"chicago":"Chen, Jianyu, Vadim Kaloshin, and Hong Kun Zhang. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04837-z.","mla":"Chen, Jianyu, et al. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics, Springer Nature, 2023, doi:10.1007/s00220-023-04837-z.","short":"J. Chen, V. Kaloshin, H.K. Zhang, Communications in Mathematical Physics (2023).","ista":"Chen J, Kaloshin V, Zhang HK. 2023. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics.","apa":"Chen, J., Kaloshin, V., & Zhang, H. K. (2023). Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04837-z","ieee":"J. Chen, V. Kaloshin, and H. K. Zhang, “Length spectrum rigidity for piecewise analytic Bunimovich billiards,” Communications in Mathematical Physics. Springer Nature, 2023.","ama":"Chen J, Kaloshin V, Zhang HK. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. 2023. doi:10.1007/s00220-023-04837-z"},"publication":"Communications in Mathematical Physics","article_type":"original","date_published":"2023-09-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14427","title":"Length spectrum rigidity for piecewise analytic Bunimovich billiards","status":"public","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In the paper, we establish Squash Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich squash-type stadia whose convex arcs are homothetic. We also establish Stadium Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich stadia whose flat boundaries are a priori fixed. In addition, for smooth Bunimovich squash-type stadia we compute the Lyapunov exponents along the maximal period two orbit, as well as the value of the Peierls’ Barrier function from the maximal marked length spectrum associated to the rotation number 2n/4n+1."}]},{"author":[{"last_name":"Ambrus","first_name":"Áron","full_name":"Ambrus, Áron"},{"first_name":"Mónika","last_name":"Csikós","full_name":"Csikós, Mónika"},{"first_name":"Gergely","last_name":"Kiss","full_name":"Kiss, Gergely"},{"first_name":"János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"},{"full_name":"Somlai, Gábor","last_name":"Somlai","first_name":"Gábor"}],"date_created":"2023-10-29T23:01:18Z","date_updated":"2023-12-13T13:04:55Z","volume":34,"year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"World Scientific Publishing","month":"10","publication_identifier":{"issn":["0129-0541"],"eissn":["1793-6373"]},"doi":"10.1142/S012905412342008X","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.11637","open_access":"1"}],"external_id":{"arxiv":["2205.11637"],"isi":["001080874400001"]},"oa":1,"isi":1,"quality_controlled":"1","abstract":[{"text":"Given a triangle Δ, we study the problem of determining the smallest enclosing and largest embedded isosceles triangles of Δ with respect to area and perimeter. This problem was initially posed by Nandakumar [17, 22] and was first studied by Kiss, Pach, and Somlai [13], who showed that if Δ′ is the smallest area isosceles triangle containing Δ, then Δ′ and Δ share a side and an angle. In the present paper, we prove that for any triangle Δ, every maximum area isosceles triangle embedded in Δ and every maximum perimeter isosceles triangle embedded in Δ shares a side and an angle with Δ. Somewhat surprisingly, the case of minimum perimeter enclosing triangles is different: there are infinite families of triangles Δ whose minimum perimeter isosceles containers do not share a side and an angle with Δ.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14464","title":"Optimal embedded and enclosing isosceles triangles","status":"public","intvolume":" 34","day":"05","article_processing_charge":"No","scopus_import":"1","date_published":"2023-10-05T00:00:00Z","publication":"International Journal of Foundations of Computer Science","citation":{"ama":"Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 2023;34(7):737-760. doi:10.1142/S012905412342008X","ista":"Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. 2023. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 34(7), 737–760.","ieee":"Á. Ambrus, M. Csikós, G. Kiss, J. Pach, and G. Somlai, “Optimal embedded and enclosing isosceles triangles,” International Journal of Foundations of Computer Science, vol. 34, no. 7. World Scientific Publishing, pp. 737–760, 2023.","apa":"Ambrus, Á., Csikós, M., Kiss, G., Pach, J., & Somlai, G. (2023). Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S012905412342008X","mla":"Ambrus, Áron, et al. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science, vol. 34, no. 7, World Scientific Publishing, 2023, pp. 737–60, doi:10.1142/S012905412342008X.","short":"Á. Ambrus, M. Csikós, G. Kiss, J. Pach, G. Somlai, International Journal of Foundations of Computer Science 34 (2023) 737–760.","chicago":"Ambrus, Áron, Mónika Csikós, Gergely Kiss, János Pach, and Gábor Somlai. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2023. https://doi.org/10.1142/S012905412342008X."},"article_type":"original","page":"737-760"},{"scopus_import":"1","day":"25","article_processing_charge":"Yes","has_accepted_license":"1","article_type":"original","publication":"Frontiers in Microbiology","citation":{"apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002","ieee":"D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002."},"date_published":"2023-09-25T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices."}],"status":"public","ddc":["000"],"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","intvolume":" 14","_id":"14449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":505078,"creator":"dernst","file_name":"2023_FrontiersMicrobiology_DElia.pdf","access_level":"open_access","date_updated":"2023-10-30T13:38:48Z","date_created":"2023-10-30T13:38:48Z","checksum":"6c0acdd8fa111a699826957b8dff19d5","success":1,"relation":"main_file","file_id":"14471"}],"month":"09","publication_identifier":{"eissn":["1664-302X"]},"quality_controlled":"1","isi":1,"oa":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"},"external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1257002","article_number":"1257002","file_date_updated":"2023-10-30T13:38:48Z","publication_status":"published","department":[{"_id":"ScienComp"}],"publisher":"Frontiers","acknowledgement":"This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.","year":"2023","pmid":1,"date_updated":"2023-12-13T13:07:21Z","date_created":"2023-10-22T22:01:16Z","volume":14,"author":[{"full_name":"D’Elia, Domenica","last_name":"D’Elia","first_name":"Domenica"},{"full_name":"Truu, Jaak","last_name":"Truu","first_name":"Jaak"},{"full_name":"Lahti, Leo","last_name":"Lahti","first_name":"Leo"},{"full_name":"Berland, Magali","last_name":"Berland","first_name":"Magali"},{"full_name":"Papoutsoglou, Georgios","last_name":"Papoutsoglou","first_name":"Georgios"},{"full_name":"Ceci, Michelangelo","first_name":"Michelangelo","last_name":"Ceci"},{"full_name":"Zomer, Aldert","last_name":"Zomer","first_name":"Aldert"},{"last_name":"Lopes","first_name":"Marta B.","full_name":"Lopes, Marta B."},{"full_name":"Ibrahimi, Eliana","first_name":"Eliana","last_name":"Ibrahimi"},{"last_name":"Gruca","first_name":"Aleksandra","full_name":"Gruca, Aleksandra"},{"full_name":"Nechyporenko, Alina","last_name":"Nechyporenko","first_name":"Alina"},{"full_name":"Frohme, Marcus","first_name":"Marcus","last_name":"Frohme"},{"full_name":"Klammsteiner, Thomas","first_name":"Thomas","last_name":"Klammsteiner"},{"last_name":"Pau","first_name":"Enrique Carrillo De Santa","full_name":"Pau, Enrique Carrillo De Santa"},{"full_name":"Marcos-Zambrano, Laura Judith","last_name":"Marcos-Zambrano","first_name":"Laura Judith"},{"last_name":"Hron","first_name":"Karel","full_name":"Hron, Karel"},{"full_name":"Pio, Gianvito","first_name":"Gianvito","last_name":"Pio"},{"first_name":"Andrea","last_name":"Simeon","full_name":"Simeon, Andrea"},{"first_name":"Ramona","last_name":"Suharoschi","full_name":"Suharoschi, Ramona"},{"full_name":"Moreno-Indias, Isabel","last_name":"Moreno-Indias","first_name":"Isabel"},{"last_name":"Temko","first_name":"Andriy","full_name":"Temko, Andriy"},{"full_name":"Nedyalkova, Miroslava","first_name":"Miroslava","last_name":"Nedyalkova"},{"last_name":"Apostol","first_name":"Elena Simona","full_name":"Apostol, Elena Simona"},{"full_name":"Truică, Ciprian Octavian","last_name":"Truică","first_name":"Ciprian Octavian"},{"full_name":"Shigdel, Rajesh","first_name":"Rajesh","last_name":"Shigdel"},{"last_name":"Telalović","first_name":"Jasminka Hasić","full_name":"Telalović, Jasminka Hasić"},{"last_name":"Bongcam-Rudloff","first_name":"Erik","full_name":"Bongcam-Rudloff, Erik"},{"first_name":"Piotr","last_name":"Przymus","full_name":"Przymus, Piotr"},{"first_name":"Naida Babić","last_name":"Jordamović","full_name":"Jordamović, Naida Babić"},{"full_name":"Falquet, Laurent","last_name":"Falquet","first_name":"Laurent"},{"first_name":"Sonia","last_name":"Tarazona","full_name":"Tarazona, Sonia"},{"full_name":"Sampri, Alexia","last_name":"Sampri","first_name":"Alexia"},{"full_name":"Isola, Gaetano","first_name":"Gaetano","last_name":"Isola"},{"full_name":"Pérez-Serrano, David","first_name":"David","last_name":"Pérez-Serrano"},{"first_name":"Vladimir","last_name":"Trajkovik","full_name":"Trajkovik, Vladimir"},{"full_name":"Klucar, Lubos","first_name":"Lubos","last_name":"Klucar"},{"first_name":"Tatjana","last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana"},{"full_name":"Havulinna, Aki S.","last_name":"Havulinna","first_name":"Aki S."},{"full_name":"Jansen, Christian","last_name":"Jansen","first_name":"Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2"},{"full_name":"Bertelsen, Randi J.","last_name":"Bertelsen","first_name":"Randi J."},{"full_name":"Claesson, Marcus Joakim","last_name":"Claesson","first_name":"Marcus Joakim"}]},{"external_id":{"arxiv":["2209.01159"],"isi":["001016927100012"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"doi":"10.1103/physreva.107.062404","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","year":"2023","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"first_name":"Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan"},{"orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A"},{"first_name":"Richard","last_name":"Kueng","full_name":"Kueng, Richard"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-12-13T14:47:25Z","date_created":"2023-06-07T06:57:32Z","volume":107,"article_number":"062404","file_date_updated":"2023-06-13T07:28:36Z","ec_funded":1,"publication":"Physical Review A","citation":{"chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404.","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404"},"article_type":"original","date_published":"2023-06-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13125","status":"public","ddc":["530"],"title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","intvolume":" 107","file":[{"creator":"dernst","file_size":2524611,"content_type":"application/pdf","file_name":"2023_PhysRevA_Sack.pdf","access_level":"open_access","date_updated":"2023-06-13T07:28:36Z","date_created":"2023-06-13T07:28:36Z","success":1,"checksum":"0d71423888eeccaa60d8f41197f26306","file_id":"13131","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"issue":"6"},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","citation":{"ieee":"U. Wagner and P. Wild, “Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes,” Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 675–717, 2023.","apa":"Wagner, U., & Wild, P. (2023). Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2521-9","ista":"Wagner U, Wild P. 2023. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 256(2), 675–717.","ama":"Wagner U, Wild P. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 2023;256(2):675-717. doi:10.1007/s11856-023-2521-9","chicago":"Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-023-2521-9.","short":"U. Wagner, P. Wild, Israel Journal of Mathematics 256 (2023) 675–717.","mla":"Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 675–717, doi:10.1007/s11856-023-2521-9."},"publication":"Israel Journal of Mathematics","page":"675-717","article_type":"original","date_published":"2023-09-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We prove the following quantitative Borsuk–Ulam-type result (an equivariant analogue of Gromov’s Topological Overlap Theorem): Let X be a free ℤ/2-complex of dimension d with coboundary expansion at least ηk in dimension 0 ≤ k < d. Then for every equivariant map F: X →ℤ/2 ℝd, the fraction of d-simplices σ of X with 0 ∈ F (σ) is at least 2−d Π d−1k=0ηk.\r\n\r\nAs an application, we show that for every sufficiently thick d-dimensional spherical building Y and every map f: Y → ℝ2d, we have f(σ) ∩ f(τ) ≠ ∅ for a constant fraction μd > 0 of pairs {σ, τ} of d-simplices of Y. In particular, such complexes are non-embeddable into ℝ2d, which proves a conjecture of Tancer and Vorwerk for sufficiently thick spherical buildings.\r\n\r\nWe complement these results by upper bounds on the coboundary expansion of two families of simplicial complexes; this indicates some limitations to the bounds one can obtain by straighforward applications of the quantitative Borsuk–Ulam theorem. Specifically, we prove\r\n\r\n• an upper bound of (d + 1)/2d on the normalized (d − 1)-th coboundary expansion constant of complete (d + 1)-partite d-dimensional complexes (under a mild divisibility assumption on the sizes of the parts); and\r\n\r\n• an upper bound of (d + 1)/2d + ε on the normalized (d − 1)-th coboundary expansion of the d-dimensional spherical building associated with GLd+2(Fq) for any ε > 0 and sufficiently large q. This disproves, in a rather strong sense, a conjecture of Lubotzky, Meshulam and Mozes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14445","intvolume":" 256","ddc":["510"],"title":"Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes","status":"public","oa_version":"Published Version","file":[{"date_updated":"2023-10-31T11:20:31Z","date_created":"2023-10-31T11:20:31Z","success":1,"checksum":"fbb05619fe4b650f341cc730425dd9c3","file_id":"14475","relation":"main_file","creator":"dernst","file_size":623787,"content_type":"application/pdf","file_name":"2023_IsraelJourMath_Wagner.pdf","access_level":"open_access"}],"publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"month":"09","oa":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"},"external_id":{"isi":["001081646400010"]},"isi":1,"quality_controlled":"1","doi":"10.1007/s11856-023-2521-9","language":[{"iso":"eng"}],"file_date_updated":"2023-10-31T11:20:31Z","year":"2023","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"first_name":"Pascal","last_name":"Wild","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","full_name":"Wild, Pascal"}],"volume":256,"date_created":"2023-10-22T22:01:14Z","date_updated":"2023-12-13T13:09:07Z"},{"oa_version":"Published Version","_id":"14447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana","abstract":[{"lang":"eng","text":"Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.\r\nHerein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes."}],"type":"journal_article","date_published":"2023-10-13T00:00:00Z","citation":{"ista":"Bieleszová K, Hladík P, Kubala M, Napier R, Brunoni F, Gelová Z, Fiedler L, Kulich I, Strnad M, Doležal K, Novák O, Friml J, Žukauskaitė A. 2023. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation.","ieee":"K. Bieleszová et al., “New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana,” Plant Growth Regulation. Springer Nature, 2023.","apa":"Bieleszová, K., Hladík, P., Kubala, M., Napier, R., Brunoni, F., Gelová, Z., … Žukauskaitė, A. (2023). New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. Springer Nature. https://doi.org/10.1007/s10725-023-01083-0","ama":"Bieleszová K, Hladík P, Kubala M, et al. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. 2023. doi:10.1007/s10725-023-01083-0","chicago":"Bieleszová, Kristýna, Pavel Hladík, Martin Kubala, Richard Napier, Federica Brunoni, Zuzana Gelová, Lukas Fiedler, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation. Springer Nature, 2023. https://doi.org/10.1007/s10725-023-01083-0.","mla":"Bieleszová, Kristýna, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation, Springer Nature, 2023, doi:10.1007/s10725-023-01083-0.","short":"K. Bieleszová, P. Hladík, M. Kubala, R. Napier, F. Brunoni, Z. Gelová, L. Fiedler, I. Kulich, M. Strnad, K. Doležal, O. Novák, J. Friml, A. Žukauskaitė, Plant Growth Regulation (2023)."},"publication":"Plant Growth Regulation","article_type":"original","article_processing_charge":"Yes (via OA deal)","day":"13","scopus_import":"1","author":[{"last_name":"Bieleszová","first_name":"Kristýna","full_name":"Bieleszová, Kristýna"},{"full_name":"Hladík, Pavel","first_name":"Pavel","last_name":"Hladík"},{"full_name":"Kubala, Martin","first_name":"Martin","last_name":"Kubala"},{"full_name":"Napier, Richard","last_name":"Napier","first_name":"Richard"},{"full_name":"Brunoni, Federica","last_name":"Brunoni","first_name":"Federica"},{"orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana","full_name":"Gelová, Zuzana"},{"last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","last_name":"Kulich","full_name":"Kulich, Ivan"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"full_name":"Doležal, Karel","first_name":"Karel","last_name":"Doležal"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Asta","last_name":"Žukauskaitė","full_name":"Žukauskaitė, Asta"}],"date_updated":"2023-12-13T13:08:25Z","date_created":"2023-10-22T22:01:15Z","acknowledgement":"The authors would like to thank Karolína Kubiasová and Iñigo Saiz-Fernández for valuable scientific discussions. Open access publishing supported by the National Technical Library in Prague. This work was supported by the Palacký University Olomouc Young Researcher Grant Competition (JG_2020_002), by the Internal Grant Agency of Palacký University Olomouc (IGA_PrF_2023_016, IGA_PrF_2023_031), by the Ministry of Education, Youth and Sports of the Czech Republic through the European Regional Development Fund-Project Plants as a tool for sustainable global development (CZ.02.1.01/0.0/0.0/16_019/0000827) and the project Support of mobility at Palacký University Olomouc II. (CZ.02.2.69/0.0/0.0/18_053/0016919). The Biacore T200 SPR instrument was provided by the WISB Research Technology Facility within the School of Life Sciences, University of Warwick.","year":"2023","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"epub_ahead","doi":"10.1007/s10725-023-01083-0","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10725-023-01083-0"}],"oa":1,"external_id":{"isi":["001084334300001"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1573-5087"],"issn":["0167-6903"]},"month":"10"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"14635","embargo":"2024-11-30","relation":"main_file","date_updated":"2023-12-01T11:10:46Z","date_created":"2023-11-30T15:53:10Z","checksum":"068fd3570506ec42b2faa390de784bc4","file_name":"PhD_Thesis.pdf","embargo_to":"open_access","access_level":"closed","creator":"ssack","content_type":"application/pdf","file_size":11947523},{"creator":"ssack","file_size":18422964,"content_type":"application/zip","access_level":"closed","file_name":"PhD Thesis (1).zip","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","date_created":"2023-11-30T15:54:11Z","date_updated":"2023-12-01T11:10:46Z","file_id":"14636","relation":"source_file"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14622","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","status":"public","ddc":["530"],"has_accepted_license":"1","article_processing_charge":"No","day":"30","date_published":"2023-11-30T00:00:00Z","citation":{"ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023."},"page":"142","ec_funded":1,"file_date_updated":"2023-12-01T11:10:46Z","related_material":{"record":[{"id":"11471","status":"public","relation":"part_of_dissertation"},{"id":"13125","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9760"}]},"author":[{"orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan","full_name":"Sack, Stefan"}],"date_created":"2023-11-28T10:58:13Z","date_updated":"2023-12-13T14:47:25Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"month":"11","doi":"10.15479/at:ista:14622","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}]},{"month":"12","publication_identifier":{"issn":["2666-1667"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"external_id":{"pmid":["38070137"]},"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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2023.102771"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.xpro.2023.102771","article_number":"102771","ec_funded":1,"publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"SiHi"}],"year":"2023","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","pmid":1,"date_created":"2023-12-13T11:48:05Z","date_updated":"2023-12-18T08:06:14Z","volume":5,"author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"scopus_import":"1","day":"08","article_processing_charge":"No","article_type":"review","publication":"STAR Protocols","citation":{"ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2023;5(1). doi:10.1016/j.xpro.2023.102771","apa":"Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2023). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” STAR Protocols, vol. 5, no. 1. Elsevier, 2023.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2023, doi:10.1016/j.xpro.2023.102771.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols. Elsevier, 2023. https://doi.org/10.1016/j.xpro.2023.102771."},"date_published":"2023-12-08T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"issue":"1","status":"public","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","ddc":["570"],"intvolume":" 5","_id":"14683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"epub_ahead","year":"2023","acknowledgement":"The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. ","date_updated":"2023-12-18T07:53:45Z","date_created":"2023-02-02T10:45:47Z","author":[{"full_name":"Agresti, Antonio","first_name":"Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962"}],"ec_funded":1,"project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"external_id":{"arxiv":["2207.08293"]},"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,"main_file_link":[{"url":"https://doi.org/10.1007/s40072-023-00319-4","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s40072-023-00319-4","publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"month":"11","title":"Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations","ddc":["510"],"status":"public","_id":"12486","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas."}],"article_type":"original","citation":{"ieee":"A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023.","apa":"Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-023-00319-4","ista":"Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations.","ama":"Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. 2023. doi:10.1007/s40072-023-00319-4","chicago":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-023-00319-4.","short":"A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).","mla":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations, Springer Nature, 2023, doi:10.1007/s40072-023-00319-4."},"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","date_published":"2023-11-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28"},{"date_published":"2023-11-16T00:00:00Z","doi":"10.1109/TIT.2023.3334032","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.04408"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04408","open_access":"1"}],"citation":{"chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3334032.","mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory, IEEE, 2023, doi:10.1109/TIT.2023.3334032.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory (2023).","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory.","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory. IEEE, 2023.","apa":"Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2023. doi:10.1109/TIT.2023.3334032"},"oa":1,"publication":"IEEE Transactions on Information Theory","article_type":"original","quality_controlled":"1","article_processing_charge":"No","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"day":"16","month":"11","scopus_import":"1","author":[{"full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan","last_name":"Zhang"},{"last_name":"Vatedka","first_name":"Shashank","full_name":"Vatedka, Shashank"}],"oa_version":"Preprint","date_created":"2023-12-10T23:01:00Z","date_updated":"2023-12-18T07:46:45Z","year":"2023","_id":"14665","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaMo"}],"publisher":"IEEE","title":"Multiple packing: Lower bounds via error exponents","status":"public","publication_status":"epub_ahead","abstract":[{"text":"We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing.","lang":"eng"}],"type":"journal_article"},{"date_updated":"2023-12-18T09:00:00Z","date_created":"2023-12-17T23:00:54Z","volume":14372,"author":[{"full_name":"Hoffmann, Charlotte","first_name":"Charlotte","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","orcid":"0000-0003-2027-5549"},{"last_name":"Hubáček","first_name":"Pavel","full_name":"Hubáček, Pavel"},{"first_name":"Chethan","last_name":"Kamath","full_name":"Kamath, Chethan"},{"full_name":"Krňák, Tomáš","first_name":"Tomáš","last_name":"Krňák"}],"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"acknowledgement":"Home Theory of Cryptography Conference paper\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nDownload book PDF\r\nDownload book EPUB\r\nSimilar content being viewed by others\r\n\r\nSlider with three content items shown per slide. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide.\r\nPrevious slide\r\nGeneric-Group Delay Functions Require Hidden-Order Groups\r\nChapter© 2020\r\n\r\nShifted powers in Lucas–Lehmer sequences\r\nArticle30 January 2019\r\n\r\nA New Class of Trapdoor Verifiable Delay Functions\r\nChapter© 2023\r\n\r\nWeak Pseudoprimality Associated with the Generalized Lucas Sequences\r\nChapter© 2022\r\n\r\nOn the Security of Time-Lock Puzzles and Timed Commitments\r\nChapter© 2020\r\n\r\nGeneration of full cycles by a composition of NLFSRs\r\nArticle08 March 2014\r\n\r\nCryptographically Strong de Bruijn Sequences with Large Periods\r\nChapter© 2013\r\n\r\nOpen Problems on With-Carry Sequence Generators\r\nChapter© 2014\r\n\r\nGenerically Speeding-Up Repeated Squaring Is Equivalent to Factoring: Sharp Thresholds for All Generic-Ring Delay Functions\r\nChapter© 2020\r\n\r\nNext slide\r\nGo to slide 1\r\nGo to slide 2\r\nGo to slide 3\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nCharlotte Hoffmann, Pavel Hubáček, Chethan Kamath & Tomáš Krňák \r\nConference paper\r\nFirst Online: 27 November 2023\r\n83 Accesses\r\n\r\nPart of the Lecture Notes in Computer Science book series (LNCS,volume 14372)\r\n\r\nAbstract\r\nLucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\n\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\n\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.\r\n\r\nKeywords\r\nDelay functions\r\nVerifiable delay functions\r\nLucas sequences\r\nDownload conference paper PDF\r\n\r\n1 Introduction\r\nA verifiable delay function (VDF) \r\n is a function that satisfies two properties. First, it is a delay function, which means it must take a prescribed (wall) time T to compute f, irrespective of the amount of parallelism available. Second, it should be possible for anyone to quickly verify – say, given a short proof \r\n – the value of the function (even without resorting to parallelism), where by quickly we mean that the verification time should be independent of or significantly smaller than T (e.g., logarithmic in T). If we drop either of the two requirements, then the primitive turns out trivial to construct. For instance, for an appropriately chosen hash function h, the delay function \r\n defined by T-times iterated hashing of the input is a natural heuristic for an inherently sequential task which, however, seems hard to verify more efficiently than by recomputing. On the other hand, the identity function \r\n is trivial to verify but also easily computable. Designing a simple function satisfying the two properties simultaneously proved to be a nontrivial task.\r\n\r\nThe notion of VDFs was introduced in [31] and later formalised in [9]. In principle, since the task of constructing a VDF reduces to the task of incrementally-verifiable computation [9, 53], constructions of VDFs could leverage succinct non-interactive arguments of knowledge (SNARKs): take any sequentially-hard function f (for instance, iterated hashing) as the delay function and then use the SNARK on top of it as the mechanism for verifying the computation of the delay function. However, as discussed in [9], the resulting construction is not quite practical since we would rely on a general-purpose machinery of SNARKs with significant overhead.\r\n\r\nEfficient VDFs via Algebraic Delay Functions. VDFs have recently found interesting applications in design of blockchains [17], randomness beacons [43, 51], proofs of data replication [9], or short-lived zero-knowledge proofs and signatures [3]. Since efficiency is an important factor there, this has resulted in a flurry of constructions of VDFs that are tailored with application and practicality in mind. They rely on more algebraic, structured delay functions that often involve iterating an atomic operation so that one can resort to custom proof systems to achieve verifiability. These constructions involve a range of algebraic settings like the RSA or class groups [5, 8, 25, 42, 55], permutation polynomials over finite fields [9], isogenies of elliptic curves [21, 52] and, very recently, lattices [15, 28]. The constructions in [42, 55] are arguably the most practical and the mechanism that underlies their delay function is the same: carry out iterated squaring in groups of unknown order, like RSA groups [47] or class groups [12]. What distinguishes these two proposals is the way verification is carried out, i.e., how the underlying “proof of exponentiation” works: while Pietrzak [42] resorts to an LFKN-style recursive proof system [35], Wesolowski [55] uses a clever linear decomposition of the exponent.\r\n\r\nIterated Modular Squaring and Sequentiality. The delay function that underlies the VDFs in [5, 25, 42, 55] is the same, and its security relies on the conjectured sequential hardness of iterated squaring in a group of unknown order (suggested in the context of time-lock puzzles by Rivest, Shamir, and Wagner [48]). Given that the practically efficient VDFs all rely on the above single delay function, an immediate open problem is to identify additional sources of sequential hardness that are structured enough to support practically efficient verifiability.\r\n\r\n1.1 Our Approach to (Verifiable) Delay Functions\r\nIn this work, we study an alternative source of sequential hardness in the algebraic setting and use it to construct efficient verifiable delay functions. The sequentiality of our delay function relies on an atomic operation that is related to the computation of so-called Lucas sequences [29, 34, 57], explained next.\r\n\r\nLucas Sequences. A Lucas sequence is a constant-recursive integer sequence that satisfies the recurrence relation\r\n\r\nfor integers P and Q.Footnote1 Specifically, the Lucas sequences of integers \r\n and \r\n of the first and second type (respectively) are defined recursively as\r\n\r\nwith \r\n, and\r\n\r\nwith \r\n.\r\n\r\nThese sequences can be alternatively defined by the characteristic polynomial \r\n. Specifically, given the discriminant \r\n of the characteristic polynomial, one can alternatively compute the above sequences by performing operations in the extension field\r\n\r\nusing the identities\r\n\r\nwhere \r\n and its conjugate \r\n are roots of the characteristic polynomial. Since conjugation and exponentiation commute in the extension field (i.e., \r\n), computing the i-th terms of the two Lucas sequences over integers reduces to computing \r\n in the extension field, and vice versa.\r\n\r\nThe intrinsic connection between computing the terms in the Lucas sequences and that of exponentiation in the extension has been leveraged to provide alternative instantiations of public-key encryption schemes like RSA and ElGamal in terms of Lucas sequences [7, 30]. However, as we explain later, the corresponding underlying computational hardness assumptions are not necessarily equivalent.\r\n\r\nOverview of Our Delay Function. The delay function in [5, 25, 42, 55] is defined as the iterated squaring base x in a (safe) RSA groupFootnote2 modulo N:\r\n\r\nOur delay function is its analogue in the setting of Lucas sequences:\r\n\r\nAs mentioned above, computing \r\n can be carried out equivalently in the extension field \r\n using the known relationship to roots of the characteristic polynomial of the Lucas sequence. Thus, the delay function can be alternatively defined as\r\n\r\nNote that the atomic operation of our delay function is “doubling” the index of an element of the Lucas sequence modulo N (i.e., \r\n) or, equivalently, squaring in the extension field \r\n (as opposed to squaring in \r\n). Using the representation of \r\n as \r\n, squaring in \r\n can be expressed as a combination of squaring, multiplication and addition modulo N, since\r\n\r\n(1)\r\nSince \r\n is a group of unknown order (provided the factorization of N is kept secret), iterated squaring remains hard here. In fact, we show in Sect. 3.2 that iterated squaring in \r\n is at least as hard as iterated squaring for RSA moduli N. Moreover, we conjecture in Conjecture 1 that it is, in fact, strictly harder (also see discussion below on advantages of our approach).\r\n\r\nVerifying Modular Lucas Sequence. To obtain a VDF, we need to show how to efficiently verify our delay function. To this end, we show how to adapt the interactive proof of exponentiation from [42] to our setting, which then – via the Fiat-Shamir Transform [22] – yields the non-interactive verification algorithm.Footnote3 Thus, our main result is stated informally below.\r\n\r\nTheorem 1\r\n(Informally stated, see Theorem 2). Assuming sequential hardness of modular Lucas sequence, there exists statistically-sound VDF in the random-oracle model.\r\n\r\nHowever, the modification of Pietrzak’s protocol is not trivial and we have to overcome several hurdles that we face in this task, which we elaborate on in Sect. 1.2. We conclude this section with discussions about our results.\r\n\r\nAdvantage of Our Approach. Our main advantage is the reliance on a potentially weaker (sequential) hardness assumption while maintaining efficiency: we show in Sect. 3.2 that modular Lucas sequences are at least as sequentially-hard as the classical delay function given by iterated modular squaring [48]. Despite the linear recursive structure of Lucas sequences, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring (Conjecture 1). In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Even though both assumptions need the group order to be hidden, we believe that there is need for a nuanced analysis of sequential hardness assumptions in hidden order groups, especially because all current delay functions that provide sufficient structure for applications are based on iterated modular squaring. If the iterated modular squaring assumption is broken, our delay function is currently the only practical alternative in the RSA group.\r\n\r\nDelay Functions in Idealised Models. Recent works studied the relationship of group-theoretic (verifiable) delay functions to the hardness of factoring in idealised models such as the algebraic group model and the generic ring model [27, 50]. In the generic ring model, Rotem and Segev [50] showed the equivalence of straight-line delay functions in the RSA setting and factoring. Our construction gives rise to a straight-line delay function and, by their result, its sequentiality is equivalent to factoring for generic algorithms. However, their result holds only in the generic ring model and leaves the relationship between the two assumptions unresolved in the standard model.\r\n\r\nCompare this with the status of the RSA assumption and factoring. On one hand, we know that in the generic ring model, RSA and factoring are equivalent [2]. Yet, it is possible to rule out certain classes of reductions from factoring to RSA in the standard model [11]. Most importantly, despite the equivalence in the generic ring model, there is currently no reduction from factoring to RSA in the standard model and it remains one of the major open problems in number theory related to cryptography since the introduction of the RSA assumption.\r\n\r\nIn summary, speeding up iterated squaring by a non-generic algorithm could be possible (necessarily exploiting the representations of ring elements modulo N), while such an algorithm may not lead to a speed-up in the computation of modular Lucas sequences despite the result of Rotem and Segev [50].\r\n\r\n1.2 Technical Overview\r\nPietrzak’s VDF. Let \r\n be an RSA modulus where p and q are safe primes and let x be a random element from \r\n. At its core, Pietrzak’s VDF relies on the interactive protocol for the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and, in a round-by-round fashion, reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round, the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued till \r\n is obtained at which point the verifier simply checks whether \r\n using a single modular squaring.\r\n\r\nSince the challenges r are public, the protocol can be compiled into a non-interactive one using the Fiat-Shamir transform [22] and this yields a means to verify the delay function\r\n\r\nIt is worth pointing out that the choice of safe primes is crucial for proving soundness: in case the group has easy-to-find elements of small order then it becomes easy to break soundness (see, e.g., [10]).\r\n\r\nAdapting Pietrzak’s Protocol to Lucas Sequences. For a modulus \r\n and integers \r\n, recall that our delay function is defined as\r\n\r\nor equivalently\r\n\r\nfor the discriminant \r\n of the characteristic polynomial \r\n. Towards building a verification algorithm for this delay function, the natural first step is to design an interactive protocol for the statement\r\n\r\n“(N, P, Q, y, T) satisfies \r\n.”\r\n\r\nIt turns out that the interactive protocol from [42] can be adapted for this purpose. However, we encounter two technicalities in this process.\r\n\r\nDealing with elements of small order. The main problem that we face while designing our protocol is avoiding elements of small order. In the case of [42], this was accomplished by moving to the setting of signed quadratic residues [26] in which the sub-groups are all of large order. It is not clear whether a corresponding object exists for our algebraic setting. However, in an earlier draft of Pietrzak’s protocol [41], this problem was dealt with in a different manner: the prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by squaring it) with a guarantee that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nIn our setting, we cannot simply ask for the square root of the midpoint as the subgroup of \r\n we effectively work in has a different structure. Nevertheless, we can use a similar approach: for an appropriately chosen small a, we provide an a-th root of \r\n (instead of \r\n itself) to the prover in the beginning of the protocol. The prover then computes the whole sequence for \r\n. In the end, he has the a-th root of every term of the original sequence and he can recover any element of the original sequence by raising to the a-th power.\r\n\r\nSampling strong modulus. The second technicality is related to the first one. In order to ensure that we can use the above trick, we require a modulus where the small subgroups are reasonably small not only in the group \r\n but also in the extension \r\n. Thus the traditional sampling algorithms that are used to sample strong primes (e.g., [46]) are not sufficient for our purposes. However, sampling strong primes that suit our criteria can still be carried out efficiently as we show in the full version.\r\n\r\nComparing Our Technique with [8, 25]. The VDFs in [8, 25] are also inspired by [42] and, hence, faced the same problem of low-order elements. In [8], this is dealt with by amplifying the soundness at the cost of parallel repetition and hence larger proofs and extra computation. In [25], the number of repetitions of [8] is reduced significantly by introducing the following technique: The exponent of the initial instance is reduced by some parameter \r\n and at the end of an interactive phase, the verifier performs final exponentiation with \r\n, thereby weeding out potential false low-order elements in the claim. This technique differs from the approach taken in our work in the following ways: The technique from [25] works in arbitrary groups but it requires the parameter \r\n to be large and of a specific form. In particular, the VDF becomes more efficient when \r\n is larger than \r\n. In our protocol, we work in RSA groups whose modulus is the product of primes that satisfy certain conditions depending on a. This enables us to choose a parameter a that is smaller than a statistical security parameter and thereby makes the final exponentiation performed by the verifier much more efficient. Further, a can be any natural number, while \r\n must be set as powers of all small prime numbers up a certain bound in [25].\r\n\r\n1.3 More Related Work\r\nTimed Primitives. The notion of VDFs was introduced in [31] and later formalised in [9]. VDFs are closely related to the notions of time-lock puzzles [48] and proofs of sequential work [36]. Roughly speaking, a time-lock puzzle is a delay function that additionally allows efficient sampling of the output via a trapdoor. A proof of sequential work, on the other hand, is a delay “multi-function”, in the sense that the output is not necessarily unique. Constructions of time-lock puzzles are rare [6, 38, 48], and there are known limitations: e.g., that it cannot exist in the random-oracle model [36]. However, we know how to construct proofs of sequential work in the random-oracle model [1, 16, 19, 36].\r\n\r\nSince VDFs have found several applications, e.g., in the design of resource-efficient blockchains [17], randomness beacons [43, 51] and proof of data replication [9], there have been several constructions. Among them, the most notable are the iterated-squaring based construction from [8, 25, 42, 55], the permutation-polynomial based construction from [9], the isogenies-based construction from [13, 21, 52] and the construction from lattice problems [15, 28]. The constructions in [42, 55] are quite practical (see the survey [10]) and the VDF deployed in the cryptocurrency Chia is basically their construction adapted to the algebraic setting of class groups [17]. This is arguably the closest work to ours. On the other hand, the constructions from [21, 52], which work in the algebraic setting of isogenies of elliptic curves where no analogue of square and multiply is known, simply rely on “exponentiation”. Although, these constructions provide a certain form of quantum resistance, they are presently far from efficient. Freitag et al. [23] constructed VDFs from any sequentially hard function and polynomial hardness of learning with errors, the first from standard assumptions. The works of Cini, Lai, and Malavolta [15, 28] constructed the first VDF from lattice-based assumptions and conjectured it to be post-quantum secure.\r\n\r\nSeveral variants of VDFs have also been proposed. A VDF is said to be unique if the proof that is used for verification is unique [42]. Recently, Choudhuri et al. [5] constructed unique VDFs from the sequential hardness of iterated squaring in any RSA group and polynomial hardness of LWE. A VDF is tight [18] if the gap between simply computing the function and computing it with a proof is small. Yet another extension is a continuous VDF [20]. The feasibility of time-lock puzzles and proofs of sequential works were recently extended to VDFs. It was shown [50] that the latter requirement, i.e., working in a group of unknown order, is inherent in a black-box sense. It was shown in [18, 37] that there are barriers to constructing tight VDFs in the random-oracle model.\r\n\r\nVDFs also have surprising connection to complexity theory [14, 20, 33].\r\n\r\nWork Related to Lucas Sequences. Lucas sequences have long been studied in the context of number theory: see for example [45] or [44] for a survey of its applications to number theory. Its earliest application to cryptography can be traced to the \r\n factoring algorithm [56]. Constructive applications were found later thanks to the parallels with exponentiation. Several encryption and signature schemes were proposed, most notably the LUC family of encryption and signatures [30, 39]. It was later shown that some of these schemes can be broken or that the advantages it claimed were not present [7]. Other applications can be found in [32].\r\n\r\n2 Preliminaries\r\n2.1 Interactive Proof Systems\r\nInteractive Protocols. An interactive protocol consists of a pair \r\n of interactive Turing machines that are run on a common input \r\n. The first machine \r\n is the prover and is computationally unbounded. The second machine \r\n is the verifier and is probabilistic polynomial-time.\r\n\r\nIn an \r\n-round (i.e., \r\n-message) interactive protocol, in each round \r\n, first \r\n sends a message \r\n to \r\n and then \r\n sends a message \r\n to \r\n, where \r\n is a finite alphabet. At the end of the interaction, \r\n runs a (deterministic) Turing machine on input \r\n. The interactive protocol is public-coin if \r\n is a uniformly distributed random string in \r\n.\r\n\r\nInteractive Proof Systems. The notion of an interactive proof for a language L is due to Goldwasser, Micali and Rackoff [24].\r\n\r\nDefinition 1\r\nFor a function \r\n, an interactive protocol \r\n is an \r\n-statistically-sound interactive proof system for L if:\r\n\r\nCompleteness: For every \r\n, if \r\n interacts with \r\n on common input \r\n, then \r\n accepts with probability 1.\r\n\r\nSoundness: For every \r\n and every (computationally-unbounded) cheating prover strategy \r\n, the verifier \r\n accepts when interacting with \r\n with probability less than \r\n, where \r\n is called the soundness error.\r\n\r\n2.2 Verifiable Delay Functions\r\nWe adapt the definition of verifiable delay functions from [9] but we decouple the verifiability and sequentiality properties for clarity of exposition of our results. First, we present the definition of a delay function.\r\n\r\nDefinition 2\r\nA delay function \r\n consists of a triple of algorithms with the following syntax:\r\n\r\n:\r\n\r\nOn input a security parameter \r\n, the algorithm \r\n outputs public parameters \r\n.\r\n\r\n:\r\n\r\nOn input public parameters \r\n and a time parameter \r\n, the algorithm \r\n outputs a challenge x.\r\n\r\n:\r\n\r\nOn input a challenge pair (x, T), the (deterministic) algorithm \r\n outputs the value y of the delay function in time T.\r\n\r\nThe security property required of a delay function is sequential hardness as defined below.\r\n\r\nDefinition 3\r\n(Sequentiality). We say that a delay function \r\n satisfies the sequentiality property, if there exists an \r\n such that for all \r\n and for every adversary \r\n, where \r\n uses \r\n processors and runs in time \r\n, there exists a negligible function \r\n such that\r\n\r\nfigure a\r\nA few remarks about our definition of sequentiality are in order:\r\n\r\n1.\r\nWe require computing \r\n to be hard in less than T sequential steps even using any polynomially-bounded amount of parallelism and precomputation. Note that it is necessary to bound the amount of parallelism, as an adversary could otherwise break the underlying hardness assumption (e.g. hardness of factorization). Analogously, T should be polynomial in \r\n as, otherwise, breaking the underlying hardness assumptions becomes easier than computing \r\n itself for large values of T.\r\n\r\n2.\r\nAnother issue is what bound on the number of sequential steps of the adversary should one impose. For example, the delay function based on T repeated modular squarings can be computed in sequential time \r\n using polynomial parallelism [4]. Thus, one cannot simply bound the sequential time of the adversary by o(T). Similarly to [38], we adapt the \r\n bound for \r\n which, in particular, is asymptotically smaller than \r\n.\r\n\r\n3.\r\nWithout loss of generality, we assume that the size of \r\n is at least linear in n and the adversary A does not have to get the unary representation of the security parameter \r\n as its input.\r\n\r\nThe definition of verifiable delay function extends a delay function with the possibility to compute publicly-verifiable proofs of correctness of the output value.\r\n\r\nDefinition 4\r\nA delay function \r\n is a verifiable delay function if it is equipped with two additional algorithms \r\n and \r\n with the following syntax:\r\n\r\n:\r\n\r\nOn input public parameters and a challenge pair (x, T), the \r\n algorithm outputs \r\n, where \r\n is a proof that the output y is the output of \r\n.\r\n\r\n:\r\n\r\nOn input public parameters, a challenge pair (x, T), and an output/proof pair \r\n, the (deterministic) algorithm \r\n outputs either \r\n or \r\n.\r\n\r\nIn addition to sequentiality (inherited from the underlying delay function), the \r\n and \r\n algorithms must together satisfy correctness and (statistical) soundness as defined below.\r\n\r\nDefinition 5\r\n(Correctness). A verifiable delay function \r\n is correct if for all \r\n\r\nfigure b\r\nDefinition 6\r\n(Statistical soundness). A verifiable delay function \r\n is statistically sound if for every (computationally unbounded) malicious prover \r\n there exists a negligible function \r\n such that for all \r\n\r\nfigure c\r\n3 Delay Functions from Lucas Sequences\r\nIn this section, we propose a delay function based on Lucas sequences and prove its sequentiality assuming that iterated squaring in a group of unknown order is sequential (Sect. 3.1). Further, we conjecture (Sect. 3.2) that our delay function candidate is even more robust than its predecessor proposed by Rivest, Shamir, and Wagner [48]. Finally, we turn our delay function candidate into a verifiable delay function (Sect. 4).\r\n\r\n3.1 The Atomic Operation\r\nOur delay function is based on subsequences of Lucas sequences, whose indexes are powers of two. Below, we use \r\n to denote the set of non-negative integers.\r\n\r\nDefinition 7\r\nFor integers \r\n, the Lucas sequences \r\n and \r\n are defined for all \r\n as\r\n\r\nwith \r\n and \r\n, and\r\n\r\nwith \r\n and \r\n.\r\n\r\nWe define subsequences \r\n, respectively \r\n, of \r\n, respectively \r\n for all \r\n as\r\n\r\n(2)\r\nAlthough the value of \r\n depends on parameters (P, Q), we omit (P, Q) from the notation because these parameters will be always obvious from the context.\r\n\r\nThe underlying atomic operation for our delay function is\r\n\r\nThere are several ways to compute \r\n in T sequential steps, and we describe two of them below.\r\n\r\nAn Approach Based on Squaring in a Suitable Extension Ring. To compute the value \r\n, we can use the extension ring \r\n, where \r\n is the discriminant of the characteristic polynomial \r\n of the Lucas sequence. The characteristic polynomial f(z) has a root \r\n, and it is known that, for all \r\n, it holds that\r\n\r\nThus, by iterated squaring of \r\n, we can compute terms of our target subsequences. To get a better understanding of squaring in the extension ring, consider the representation of the root \r\n for some \r\n. Then,\r\n\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(3)\r\nAn Approach Based on Known Identities. Many useful identities for members of modular Lucas sequences are known, such as\r\n\r\n(4)\r\nSetting \r\n we get\r\n\r\n(5)\r\nThe above identities are not hard to derive (see, e.g., Lemma 12.5 in [40]). Indexes are doubled on each of application of the identities in Eq. (5), and, thus, for \r\n, we define an auxiliary sequence \r\n by \r\n. Using the identities in Eq. (5), we get recursive equations\r\n\r\n(6)\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(7)\r\nAfter a closer inspection, the reader may have an intuition that an auxiliary sequence \r\n, which introduces a third state variable, is redundant. This intuition is indeed right. In fact, there is another easily derivable identity\r\n\r\n(8)\r\nwhich can be found, e.g., as Lemma 12.2 in [40]. On the other hand, Eq. (8) is quite interesting because it allows us to compute large powers of an element \r\n using two Lucas sequences. We use this fact in the security reduction in Sect. 3.2. Our construction of a delay function, denoted \r\n, is given in Fig. 1.\r\n\r\nFig. 1.\r\nfigure 1\r\nOur delay function candidate \r\n based on a modular Lucas sequence.\r\n\r\nFull size image\r\nOn the Discriminant D. Notice that whenever D is a quadratic residue modulo N, the value \r\n is an element of \r\n and hence \r\n. By definition, LCS.Gen generates a parameter D that is a quadratic residue with probability 1/4, so it might seem that in one fourth of the cases there is another approach to compute \r\n: find the element \r\n and then perform n sequential squarings in the group \r\n. However, it is well known that finding square roots of uniform elements in \r\n is equivalent to factoring the modulus N, so this approach is not feasible. We can therefore omit any restrictions on the discriminant D in the definition of our delay function LCS.\r\n\r\n3.2 Reduction from RSW Delay Function\r\nIn order to prove the sequentiality property (Definition 3) of our candidate \r\n, we rely on the standard conjecture of the sequentiality of the \r\n time-lock puzzles, implicitly stated in [48] as the underlying hardness assumption.\r\n\r\nDefinition 8\r\n(\r\n delay function). The \r\n delay function is defined as follows:\r\n\r\n: Samples two n-bit primes p and q and outputs \r\n.\r\n\r\n: Outputs an x sampled from the uniform distribution on \r\n.\r\n\r\n: Outputs \r\n.\r\n\r\nTheorem 2\r\nIf the \r\n delay function has the sequentiality property, then the \r\n delay function has the sequentiality property.\r\n\r\nProof\r\nSuppose there exists an adversary \r\n who contradicts the sequentiality of \r\n, where \r\n is a precomputation algorithm and \r\n is an online algorithm. We construct an adversary \r\n who contradicts the sequentiality of \r\n as follows:\r\n\r\nThe algorithm \r\n is defined identically to the algorithm \r\n.\r\n\r\nOn input \r\n, \r\n picks a P from the uniform distribution on \r\n, sets\r\n\r\nand it runs \r\n to compute \r\n. The algorithm \r\n computes \r\n using the identity in Eq. (8).\r\n\r\nNote that the input distribution for the algorithm \r\n produced by \r\n differs from the one produced by \r\n, because the \r\n generator samples Q from the uniform distribution on \r\n (instead of \r\n). However, this is not a problem since the size of \r\n is negligible compared to the size of \r\n, so the statistical distance between the distribution of D produced by \r\n and the distribution of D sampled by \r\n is negligible in the security parameter. Thus, except for a negligible multiplicative loss, the adversary \r\n attains the same success probability of breaking the sequentiality of \r\n as the probability of \r\n breaking the sequentiality of \r\n – a contradiction to the assumption of the theorem. \r\n\r\nWe believe that the converse implication to Theorem 2 is not true, i.e., that breaking the sequentiality of \r\n does not necessarily imply breaking the sequentiality of \r\n. Below, we state it as a conjecture.\r\n\r\nConjecture 1\r\nSequentiality of \r\n cannot be reduced to sequentiality of \r\n.\r\n\r\nOne reason why the above conjecture might be true is that, while the \r\n delay function is based solely only on multiplication in the group \r\n, our \r\n delay function uses the full arithmetic (addition and multiplication) of the commutative ring \r\n.\r\n\r\nOne way to support the conjecture would be to construct an algorithm that speeds up iterated squaring but is not immediately applicable to Lucas sequences. By [49] we know that this cannot be achieved by a generic algorithm. A non-generic algorithm that solves iterated squaring in time \r\n is presented in [4]. The main tool of their construction is the Explicit Chinese Remainder Theorem modulo N. However, a similiar theorem exists also for univariate polynomial rings, which suggests that a similar speed-up can be obtained for our delay function by adapting the techniques in [4] to our setting.\r\n\r\n4 VDF from Lucas Sequences\r\nIn Sect. 3.1 we saw different ways of computing the atomic operation of the delay function. Computing \r\n in the extension field seems to be the more natural and time and space effective approach. Furthermore, writing the atomic operation \r\n as \r\n is very clear, and, thus, we follow this approach throughout the rest of the paper.\r\n\r\n4.1 Structure of \r\nTo construct a VDF based on Lucas sequences, we use an algebraic extension\r\n\r\n(9)\r\nwhere N is an RSA modulus and \r\n. In this section, we describe the structure of the algebraic extension given in Expression (9). Based on our understanding of the structure of the above algebraic extension, we can conclude that using modulus N composed of safe primes (i.e., for all prime factors p of N, \r\n has a large prime divisor) is necessary but not sufficient condition for security of our construction. We specify some sufficient conditions on factors of N in the subsequent Sect. 4.2.\r\n\r\nFirst, we introduce some simplifying notation for quotient rings.\r\n\r\nDefinition 9\r\nFor \r\n and \r\n, we denote by \r\n the quotient ring \r\n, where (m, f(x)) denotes the ideal of the ring \r\n generated by m and f(x).\r\n\r\nObservation 1, below, allows us to restrict our analysis only to the structure of \r\n for prime \r\n.\r\n\r\nObservation 1\r\nLet \r\n be distinct primes, \r\n and \r\n. Then\r\n\r\nProof\r\nUsing the Chinese reminder theorem, we get\r\n\r\nas claimed. \r\n\r\nThe following lemma characterizes the structure of \r\n with respect to the discriminant of f. We use \r\n to denote the standard Legendre symbol.\r\n\r\nLemma 1\r\nLet \r\n and \r\n be a polynomial of degree 2 with the discriminant D. Then\r\n\r\nProof\r\nWe consider each case separately:\r\n\r\nIf \r\n, then f(x) is irreducible over \r\n and \r\n is a field with \r\n elements. Since \r\n is a finite field, \r\n is cyclic and contains \r\n elements.\r\n\r\nIf \r\n, then \r\n and f has some double root \r\n and it can be written as \r\n for some \r\n. Since the ring \r\n is isomorphic to the ring \r\n (consider the isomorphism \r\n), we can restrict ourselves to describing the structure of \r\n.\r\n\r\nWe will prove that the function \r\n,\r\n\r\nis an isomorphism. First, the polynomial \r\n is invertible if and only if \r\n (inverse is \r\n). For the choice \r\n, we have\r\n\r\nThus \r\n is onto. Second, \r\n is, in fact, a bijection, because\r\n\r\n(10)\r\nFinally, \r\n is a homomorphism, because\r\n\r\nIf \r\n, then f(x) has two roots \r\n. We have an isomorphism\r\n\r\nand \r\n. \r\n\r\n4.2 Strong Groups and Strong Primes\r\nTo achieve the verifiability property of our construction, we need \r\n to contain a strong subgroup (defined next) of order asymptotically linear in p. We remark that our definition of strong primes is stronger than the one by Rivest and Silverman [46].\r\n\r\nDefinition 10\r\n(Strong groups). For \r\n, we say that a non-trivial group \r\n is \r\n-strong, if the order of each non-trivial subgroup of \r\n is greater than \r\n.\r\n\r\nObservation 2\r\nIf \r\n and \r\n are \r\n-strong groups, then \r\n is a \r\n-strong group.\r\n\r\nIt can be seen from Lemma 1 that \r\n always contains groups of small order (e.g. \r\n). To avoid these, we descend into the subgroup of a-th powers of elements of \r\n. Below, we introduce the corresponding notation.\r\n\r\nDefinition 11\r\nFor an Abelian group \r\n and \r\n, we define the subgroup \r\n of \r\n in the multiplicative notation and \r\n in the additive notation.\r\n\r\nFurther, we show in Lemma 2 below that \r\n-strong primality (defined next) is a sufficient condition for \r\n to be a \r\n-strong group.\r\n\r\nDefinition 12\r\n(Strong primes). Let \r\n and \r\n. We say that p is a \r\n-strong prime, if \r\n and there exists \r\n, \r\n, such that \r\n and every prime factor of W is greater than \r\n.\r\n\r\nSince a is a public parameter in our setup, super-polynomial a could reveal partial information about the factorization of N. However, we could allow a to be polynomial in \r\n while maintaining hardness of factoring N.Footnote4 For the sake of simplicity of Definition 12, we rather use stronger condition \r\n. The following simple observation will be useful for proving Lemma 2.\r\n\r\nObservation 3\r\nFor \r\n.\r\n\r\nLemma 2\r\nLet p be a \r\n-strong prime and \r\n be a quadratic polynomial. Then, \r\n is a \r\n-strong group.\r\n\r\nProof\r\nFrom definition of the strong primes, there exists \r\n, whose factors are bigger than \r\n and \r\n. We denote \r\n a factor of W. Applying Observation 3 to Lemma 1, we get\r\n\r\nIn particular, we used above the fact that Observation 2 implies that \r\n as explained next. Since \r\n, all divisors of \r\n are divisors of aW. By definition of a and W in Definition 12, we also have that \r\n, which implies that any factor of \r\n divides either a or W, but not both. When we divide \r\n by all the common divisors with a, only the common divisors with W are left, which implies \r\n. The proof of the lemma is now completed by Observation 2.\r\n\r\nCorollary 1\r\nLet p be a \r\n-strong prime, q be a \r\n-strong prime, \r\n, \r\n, \r\n and \r\n. Then \r\n is \r\n-strong.\r\n\r\n4.3 Our Interactive Protocol\r\nOur interactive protocol is formally described in Fig. 3. To understand this protocol, we first recall the outline of Pietrzak’s interactive protocol from Sect. 1.2 and then highlight the hurdles. Let \r\n be an RSA modulus where p and q are strong primes and let x be a random element from \r\n. The interactive protocol in [42] allows a prover to convince the verifier of the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and in a round-by-round fashion reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued until \r\n is obtained at which point the verifier simply checks whether \r\n.\r\n\r\nThe main problem, we face while designing our protocol is ensuring that the verifier can check whether \r\n sent by prover lies in an appropriate subgroup of \r\n. In the first draft of Pietrzak’s protocol [41], prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by simply squaring it) with a guarantee, that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nUsing Pietrzak’s protocol directly for our delay function would require computing a-th roots in RSA group for some arbitrary a. Since this is a computationally hard problem, we cannot use the same trick. In fact, the VDF construction of Wesolowski [54] is based on similar hardness assumption.\r\n\r\nWhile Pietrzak shifted from \r\n to the group of signed quadratic residues \r\n in his following paper [42] to get unique proofs, we resort to his old idea of ‘squaring a square root’ and generalise it.\r\n\r\nThe high level idea is simple. First, on input \r\n, prover computes the sequence \r\n. Next, during the protocol, verifier maps all elements sent by the prover by homomorphism\r\n\r\n(11)\r\ninto the target strong group \r\n. This process is illustrated in Fig. 2. Notice that the equality \r\n for the original sequence implies the equality \r\n for the mapped sequence \r\n.\r\n\r\nFig. 2.\r\nfigure 2\r\nIllustration of our computation of the iterated squaring using the a-th root of \r\n. Horizontal arrows are \r\n and diagonal arrows are \r\n.\r\n\r\nFull size image\r\nRestriction to Elements of \r\n. Mapping Eq. (11) introduces a new technical difficulty. Since \r\n is not injective, we narrow the domain inputs, for which the output of our VDF is verifiable, from \r\n to \r\n. Furthermore, the only way to verify that a certain x is an element of \r\n is to get an a-th root of x and raise it to the ath power. So we have to represent elements of \r\n by elements of \r\n anyway. To resolve these two issues, we introduce a non-unique representation of elements of \r\n.\r\n\r\nDefinition 13\r\nFor \r\n and \r\n, we denote \r\n (an element of \r\n) by [x]. Since this representation of \r\n is not unique, we define an equality relation by\r\n\r\nWe will denote by tilde () the elements that were already powered to the a by a verifier (i.e. ). Thus tilded variables verifiably belong to the target group \r\n.\r\n\r\nIn the following text, the goal of the brackets notation in Definition 13 is to distinguish places where the equality means the equality of elements of \r\n from those places, where the equality holds up to \r\n. A reader can also see the notation in Definition 13 as a concrete representation of elements of a factor group \r\n.\r\n\r\nOur security reduction 2 required the delay function to operate everywhere on \r\n. This is not a problem if the \r\n algorithm is modified to output the set \r\n.\r\n\r\nFig. 3.\r\nfigure 3\r\nOur Interactive Protocol for \r\n.\r\n\r\nFull size image\r\n4.4 Security\r\nRecall here that \r\n is \r\n-strong group, so there exist\r\n\r\n and \r\n such that\r\n\r\n(12)\r\nDefinition 14\r\nFor \r\n and \r\n, we define \r\n as i-th coordinate of \r\n, where \r\n is the isomorphism given by Eq. (12).\r\n\r\nLemma 3\r\nLet \r\n and \r\n. If \r\n, then\r\n\r\n\t(13)\r\nProof\r\nFix \r\n, \r\n and y. Let some \r\n satisfy\r\n\r\n(14)\r\nUsing notation from Definition 14, we rewrite Eq. (14) as a set of equations\r\n\r\nFor every \r\n, by reordering the terms, the j-th equation becomes\r\n\r\n(15)\r\nIf \r\n, then \r\n. Further for every \r\n. It follows that \r\n. Putting these two equations together gives us \r\n, which contradicts our assumption \r\n.\r\n\r\nIt follows that there exists \r\n such that\r\n\r\n(16)\r\nThereafter there exists \r\n such that \r\n divides \r\n and\r\n\r\n(17)\r\nFurthermore, from Eq. (15), \r\n divides \r\n. Finally, dividing eq. Eq. (15) by \r\n, we get that r is determined uniquely (\r\n),\r\n\r\nUsing the fact that \r\n, this uniqueness of r upper bounds number of \r\n, such that Eq. (14) holds, to one. It follows that the probability that Eq. (14) holds for r chosen randomly from the uniform distribution over \r\n is less than \r\n. \r\n\r\nCorollary 2\r\nThe halving protocol will turn an invalid input tuple (i.e. \r\n) into a valid output tuple (i.e. \r\n) with probability less than \r\n.\r\n\r\nTheorem 3\r\nFor any computationally unbounded prover who submits anything other than \r\n such that \r\n in phase 2 of the protocol, the soundness error is upper-bounded by \r\n\r\nProof\r\nIn each round of the protocol, T decreases to \r\n. It follows that the number of rounds of the halving protocol before reaching \r\n is upper bounded by \r\n.\r\n\r\nIf the verifier accepts the solution tuple \r\n in the last round, then the equality \r\n must hold. It follows that the initial inequality must have turned into equality in some round of the halving protocol. By Lemma 3, the probability of this event is bounded by \r\n. Finally, using the union bound for all rounds, we obtain the upper bound (\r\n. \r\n\r\n4.5 Our VDF\r\nAnalogously to the VDF of Pietrzak [42], we compile our public-coin interactive proof given in Fig. 3 into a VDF using the Fiat-Shamir heuristic. The complete construction is given in Fig. 4. For ease of exposition, we assume that the time parameter T is always a power of two.\r\n\r\nFig. 4.\r\nfigure 4\r\n based on Lucas sequences\r\n\r\nFull size image\r\nAs discussed in Sect. 4.3, it is crucial for the security of the protocol that the prover computes a sequence of powers of the a-th root of the challenge and the resulting value (as well as the intermediate values) received from the prover is lifted to the appropriate group by raising it to the a-th power. We use the tilde notation in Fig. 4 in order to denote elements on the sequence relative to the a-th root.\r\n\r\nNote that, by the construction, the output of our VDF is the \r\n-th power of the root of the characteristic polynomial for Lucas sequence with parameters P and Q. Therefore, the value of the delay function implicitly corresponds to the \r\n-th term of the Lucas sequence.\r\n\r\nTheorem 4\r\nLet \r\n be the statistical security parameter. The \r\n VDF defined in Fig. 4 is correct and statistically-sound with a negligible soundness error if \r\n is modelled as a random oracle, against any adversary that makes \r\n oracle queries.\r\n\r\nProof\r\nThe correctness follows directly by construction.\r\n\r\nTo prove its statistical soundness, we proceed in a similar way to [42]. We cannot apply Fiat-Shamir transformation directly, because our protocol does not have constant number of rounds, thus we use Fiat-Shamir heuristic to each round separately.\r\n\r\nFirst, we use a random oracle as the \r\n function. Second, if a malicious prover computed a proof accepted by verifier for some tuple \r\n such that\r\n\r\n(19)\r\nthen he must have succeeded in turning inequality from Eq. (19) into equality in some round. By Lemma 3, probability of such a flipping is bounded by \r\n. Every such an attempt requires one query to random oracle. Using a union bound, it follows that the probability that a malicious prover who made q queries to random oracle succeeds in flipping initial inequality into equality in some round is upper-bounded by \r\n.\r\n\r\nSince q is \r\n, \r\n is a negligible function and thus the soundness error is negligible. \r\n\r\nNotes\r\n1.\r\nNote that integer sequences like Fibonacci numbers and Mersenne numbers are special cases of Lucas sequences.\r\n\r\n2.\r\nThe choice of modulus N is said to be safe if \r\n for safe primes \r\n and \r\n, where \r\n and \r\n are also prime.\r\n\r\n3.\r\nFurther, using the ideas from [14, 20], it is possible to construct so-called continuous VDFs from Lucas sequences.\r\n\r\n4.\r\nSince we set a to be at most polynomial in \r\n, its is possible to go over all possible candidate values for a in time polynomial in \r\n. 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Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, by the European Research Council (ERC) under the European Union’s Horizon Europe research and innovation programme (grant agreement No. 101042417, acronym SPP), and by ISF grant 1789/19.","year":"2023","month":"11","publication_identifier":{"isbn":["9783031486234"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-02","location":"Taipei, Taiwan","start_date":"2023-11-29","name":"TCC: Theory of Cryptography"},"doi":"10.1007/978-3-031-48624-1_13","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2023/1404","open_access":"1"}],"abstract":[{"text":"Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"(Verifiable) delay functions from Lucas sequences","intvolume":" 14372","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14693","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-27T00:00:00Z","page":"336-362","publication":"21st International Conference on Theory of Cryptography","citation":{"chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Tomáš Krňák. “(Verifiable) Delay Functions from Lucas Sequences.” In 21st International Conference on Theory of Cryptography, 14372:336–62. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48624-1_13.","short":"C. Hoffmann, P. Hubáček, C. Kamath, T. Krňák, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 336–362.","mla":"Hoffmann, Charlotte, et al. “(Verifiable) Delay Functions from Lucas Sequences.” 21st International Conference on Theory of Cryptography, vol. 14372, Springer Nature, 2023, pp. 336–62, doi:10.1007/978-3-031-48624-1_13.","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and T. Krňák, “(Verifiable) delay functions from Lucas sequences,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14372, pp. 336–362.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Krňák, T. (2023). (Verifiable) delay functions from Lucas sequences. In 21st International Conference on Theory of Cryptography (Vol. 14372, pp. 336–362). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48624-1_13","ista":"Hoffmann C, Hubáček P, Kamath C, Krňák T. 2023. (Verifiable) delay functions from Lucas sequences. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14372, 336–362.","ama":"Hoffmann C, Hubáček P, Kamath C, Krňák T. (Verifiable) delay functions from Lucas sequences. In: 21st International Conference on Theory of Cryptography. Vol 14372. Springer Nature; 2023:336-362. doi:10.1007/978-3-031-48624-1_13"}},{"page":"271-300","publication":"21st International Conference on Theory of Cryptography","citation":{"chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” In 21st International Conference on Theory of Cryptography, 14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10.","short":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300.","mla":"Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10.","ieee":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost of post-compromise security in concurrent Continuous Group-Key Agreement,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14371, pp. 271–300.","apa":"Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023). On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10","ista":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14371, 271–300.","ama":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300. doi:10.1007/978-3-031-48621-0_10"},"date_published":"2023-11-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","title":"On the cost of post-compromise security in concurrent Continuous Group-Key Agreement","status":"public","intvolume":" 14371","_id":"14691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.\r\nWe prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.\r\nOur lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper."}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2023/1123","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-02","location":"Taipei, Taiwan","start_date":"2023-11-29","name":"TCC: Theory of Cryptography"},"doi":"10.1007/978-3-031-48621-0_10","month":"11","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031486203"],"eissn":["1611-3349"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2023","date_created":"2023-12-17T23:00:53Z","date_updated":"2023-12-18T08:36:51Z","volume":14371,"author":[{"last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","full_name":"Auerbach, Benedikt"},{"last_name":"Cueto Noval","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel"},{"full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","first_name":"Guillermo","last_name":"Pascual Perez"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}]},{"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","year":"2023","date_created":"2023-12-17T23:00:54Z","date_updated":"2023-12-18T09:17:03Z","volume":14371,"author":[{"last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","full_name":"Auerbach, Benedikt"},{"full_name":"Hoffmann, Charlotte","first_name":"Charlotte","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","orcid":"0000-0003-2027-5549"},{"full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez","first_name":"Guillermo","orcid":"0000-0001-8630-415X","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"}],"month":"11","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031486203"],"eissn":["1611-3349"]},"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2023/808","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-48621-0_11","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions.\r\nIn this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach.\r\nThe main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.","lang":"eng"}],"title":"Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing","status":"public","intvolume":" 14371","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14692","oa_version":"Preprint","scopus_import":"1","day":"27","article_processing_charge":"No","page":"301-330","publication":"21st International Conference on Theory of Cryptography","citation":{"chicago":"Auerbach, Benedikt, Charlotte Hoffmann, and Guillermo Pascual Perez. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” In 21st International Conference on Theory of Cryptography, 14371:301–30. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_11.","mla":"Auerbach, Benedikt, et al. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 301–30, doi:10.1007/978-3-031-48621-0_11.","short":"B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 301–330.","ista":"Auerbach B, Hoffmann C, Pascual Perez G. 2023. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. 21st International Conference on Theory of Cryptography. , LNCS, vol. 14371, 301–330.","ieee":"B. Auerbach, C. Hoffmann, and G. Pascual Perez, “Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing,” in 21st International Conference on Theory of Cryptography, 2023, vol. 14371, pp. 301–330.","apa":"Auerbach, B., Hoffmann, C., & Pascual Perez, G. (2023). Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 301–330). Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_11","ama":"Auerbach B, Hoffmann C, Pascual Perez G. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:301-330. doi:10.1007/978-3-031-48621-0_11"},"date_published":"2023-11-27T00:00:00Z"},{"article_number":"205429","year":"2023","acknowledgement":"The authors are grateful to J. Karcher and A. Mirlin for collaboration on the related project. We thank I. Gruzberg and A. Mirlin for useful discussions and comments. I.S.B. is grateful to M. Parfenov and P. Ostrovsky for collaboration on the related project. The research was supported by Russian Science Foundation (Grant No. 22-42-04416).","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"full_name":"Babkin, Serafim","first_name":"Serafim","last_name":"Babkin","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","orcid":"0009-0003-7382-8036"},{"full_name":"Burmistrov, I","first_name":"I","last_name":"Burmistrov"}],"date_updated":"2023-12-18T08:45:28Z","date_created":"2023-12-17T23:00:53Z","volume":108,"month":"11","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2308.16852"}],"external_id":{"arxiv":["2308.16852"]},"quality_controlled":"1","doi":"10.1103/PhysRevB.108.205429","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction."}],"issue":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14690","status":"public","title":"Boundary multifractality in the spin quantum Hall symmetry class with interaction","intvolume":" 108","oa_version":"Preprint","scopus_import":"1","day":"15","article_processing_charge":"No","publication":"Physical Review B","citation":{"short":"S. Babkin, I. Burmistrov, Physical Review B 108 (2023).","mla":"Babkin, Serafim, and I. Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B, vol. 108, no. 20, 205429, American Physical Society, 2023, doi:10.1103/PhysRevB.108.205429.","chicago":"Babkin, Serafim, and I Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.205429.","ama":"Babkin S, Burmistrov I. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 2023;108(20). doi:10.1103/PhysRevB.108.205429","apa":"Babkin, S., & Burmistrov, I. (2023). Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.205429","ieee":"S. Babkin and I. Burmistrov, “Boundary multifractality in the spin quantum Hall symmetry class with interaction,” Physical Review B, vol. 108, no. 20. American Physical Society, 2023.","ista":"Babkin S, Burmistrov I. 2023. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 108(20), 205429."},"article_type":"original","date_published":"2023-11-15T00:00:00Z"},{"date_published":"2023-12-01T00:00:00Z","page":"2053-2055","article_type":"letter_note","citation":{"chicago":"Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-023-01595-5.","short":"E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023) 2053–2055.","mla":"Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics, vol. 55, no. 12, Springer Nature, 2023, pp. 2053–55, doi:10.1038/s41588-023-01595-5.","ieee":"E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting the use of structural similarity index in Hi-C,” Nature Genetics, vol. 55, no. 12. Springer Nature, pp. 2053–2055, 2023.","apa":"Ing-Simmons, E., Machnik, N. N., & Vaquerizas, J. M. (2023). Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-023-01595-5","ista":"Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.","ama":"Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 2023;55(12):2053-2055. doi:10.1038/s41588-023-01595-5"},"publication":"Nature Genetics","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","intvolume":" 55","title":"Reply to: Revisiting the use of structural similarity index in Hi-C","status":"public","_id":"14689","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41588-023-01595-5","quality_controlled":"1","external_id":{"pmid":["38052961"]},"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"month":"12","volume":55,"date_updated":"2023-12-18T08:51:38Z","date_created":"2023-12-17T23:00:53Z","author":[{"full_name":"Ing-Simmons, Elizabeth","last_name":"Ing-Simmons","first_name":"Elizabeth"},{"last_name":"Machnik","first_name":"Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N"},{"last_name":"Vaquerizas","first_name":"Juan M.","full_name":"Vaquerizas, Juan M."}],"publisher":"Springer Nature","department":[{"_id":"MaRo"}],"publication_status":"published","pmid":1,"year":"2023"},{"keyword":["Physical and Theoretical Chemistry"],"month":"12","day":"19","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"article_processing_charge":"No","article_type":"review","quality_controlled":"1","publication":"Faraday Discussions","citation":{"chicago":"Archer, Lynden A., Peter G. Bruce, Ernesto J. Calvo, Daniel Dewar, James H. J. Ellison, Stefan Alexander Freunberger, Xiangwen Gao, et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90062b.","mla":"Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90062b.","short":"L.A. Archer, P.G. Bruce, E.J. Calvo, D. Dewar, J.H.J. Ellison, S.A. Freunberger, X. Gao, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Menkin, S. Mondal, Q. Qiu, T. Samarakoon, I. Temprano, K. Uosaki, G. Vailaya, E.D. Wachsman, Y. Wu, S. Ye, Faraday Discussions (2023).","ista":"Archer LA, Bruce PG, Calvo EJ, Dewar D, Ellison JHJ, Freunberger SA, Gao X, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Menkin S, Mondal S, Qiu Q, Samarakoon T, Temprano I, Uosaki K, Vailaya G, Wachsman ED, Wu Y, Ye S. 2023. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions.","ieee":"L. A. Archer et al., “Towards practical metal–oxygen batteries: General discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.","apa":"Archer, L. A., Bruce, P. G., Calvo, E. J., Dewar, D., Ellison, J. H. J., Freunberger, S. A., … Ye, S. (2023). Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90062b","ama":"Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90062b"},"language":[{"iso":"eng"}],"doi":"10.1039/d3fd90062b","date_published":"2023-12-19T00:00:00Z","type":"journal_article","title":"Towards practical metal–oxygen batteries: General discussion","publication_status":"epub_ahead","status":"public","publisher":"Royal Society of Chemistry","department":[{"_id":"StFr"}],"_id":"14701","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-20T11:54:06Z","date_created":"2023-12-20T10:48:09Z","oa_version":"None","author":[{"full_name":"Archer, Lynden A.","last_name":"Archer","first_name":"Lynden A."},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."},{"first_name":"Ernesto J.","last_name":"Calvo","full_name":"Calvo, Ernesto J."},{"full_name":"Dewar, Daniel","last_name":"Dewar","first_name":"Daniel"},{"last_name":"Ellison","first_name":"James H. J.","full_name":"Ellison, James H. J."},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Gao","first_name":"Xiangwen","full_name":"Gao, Xiangwen"},{"first_name":"Laurence J.","last_name":"Hardwick","full_name":"Hardwick, Laurence J."},{"full_name":"Horwitz, Gabriela","first_name":"Gabriela","last_name":"Horwitz"},{"full_name":"Janek, Jürgen","last_name":"Janek","first_name":"Jürgen"},{"full_name":"Johnson, Lee R.","first_name":"Lee R.","last_name":"Johnson"},{"first_name":"Jack W.","last_name":"Jordan","full_name":"Jordan, Jack W."},{"full_name":"Matsuda, Shoichi","last_name":"Matsuda","first_name":"Shoichi"},{"last_name":"Menkin","first_name":"Svetlana","full_name":"Menkin, Svetlana"},{"full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","last_name":"Mondal"},{"full_name":"Qiu, Qianyuan","first_name":"Qianyuan","last_name":"Qiu"},{"last_name":"Samarakoon","first_name":"Thukshan","full_name":"Samarakoon, Thukshan"},{"full_name":"Temprano, Israel","first_name":"Israel","last_name":"Temprano"},{"full_name":"Uosaki, Kohei","last_name":"Uosaki","first_name":"Kohei"},{"first_name":"Ganesh","last_name":"Vailaya","full_name":"Vailaya, Ganesh"},{"last_name":"Wachsman","first_name":"Eric D.","full_name":"Wachsman, Eric D."},{"last_name":"Wu","first_name":"Yiying","full_name":"Wu, Yiying"},{"last_name":"Ye","first_name":"Shen","full_name":"Ye, Shen"}]},{"_id":"14702","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publisher":"Royal Society of Chemistry","department":[{"_id":"StFr"}],"status":"public","title":"Materials for stable metal–oxygen battery cathodes: general discussion","publication_status":"epub_ahead","author":[{"full_name":"Attard, Gary A.","last_name":"Attard","first_name":"Gary A."},{"full_name":"Calvo, Ernesto J.","last_name":"Calvo","first_name":"Ernesto J."},{"full_name":"Curtiss, Larry A.","first_name":"Larry A.","last_name":"Curtiss"},{"full_name":"Dewar, Daniel","last_name":"Dewar","first_name":"Daniel"},{"full_name":"Ellison, James H. J.","first_name":"James H. J.","last_name":"Ellison"},{"full_name":"Gao, Xiangwen","last_name":"Gao","first_name":"Xiangwen"},{"full_name":"Grey, Clare P.","last_name":"Grey","first_name":"Clare P."},{"first_name":"Laurence J.","last_name":"Hardwick","full_name":"Hardwick, Laurence J."},{"first_name":"Gabriela","last_name":"Horwitz","full_name":"Horwitz, Gabriela"},{"full_name":"Janek, Juergen","last_name":"Janek","first_name":"Juergen"},{"last_name":"Johnson","first_name":"Lee R.","full_name":"Johnson, Lee R."},{"full_name":"Jordan, Jack W.","first_name":"Jack W.","last_name":"Jordan"},{"first_name":"Shoichi","last_name":"Matsuda","full_name":"Matsuda, Shoichi"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"last_name":"Neale","first_name":"Alex R.","full_name":"Neale, Alex R."},{"full_name":"Ortiz-Vitoriano, Nagore","first_name":"Nagore","last_name":"Ortiz-Vitoriano"},{"first_name":"Israel","last_name":"Temprano","full_name":"Temprano, Israel"},{"first_name":"Ganesh","last_name":"Vailaya","full_name":"Vailaya, Ganesh"},{"last_name":"Wachsman","first_name":"Eric D.","full_name":"Wachsman, Eric D."},{"first_name":"Hsien-Hau","last_name":"Wang","full_name":"Wang, Hsien-Hau"},{"last_name":"Wu","first_name":"Yiying","full_name":"Wu, Yiying"},{"full_name":"Ye, Shen","first_name":"Shen","last_name":"Ye"}],"oa_version":"None","date_created":"2023-12-20T10:49:43Z","date_updated":"2023-12-20T11:58:12Z","type":"journal_article","citation":{"ista":"Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2023. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions.","apa":"Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2023). Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90059b","ieee":"G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.","ama":"Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90059b","chicago":"Attard, Gary A., Ernesto J. Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90059b.","mla":"Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90059b.","short":"G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions (2023)."},"publication":"Faraday Discussions","quality_controlled":"1","article_type":"review","doi":"10.1039/d3fd90059b","date_published":"2023-12-18T00:00:00Z","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry"],"article_processing_charge":"No","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"day":"18","month":"12"},{"_id":"14360","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","status":"public","ddc":["570"],"intvolume":" 14","oa_version":"Published Version","file":[{"file_name":"2023_NatureComm_Sitarska.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2725421,"file_id":"14365","relation":"main_file","date_created":"2023-09-25T08:22:58Z","date_updated":"2023-09-25T08:22:58Z","success":1,"checksum":"ad670e3b3c64fc585675948370f6b149"}],"type":"journal_article","abstract":[{"text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.","lang":"eng"}],"publication":"Nature Communications","citation":{"chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer Nature, 2023, doi:10.1038/s41467-023-41173-1.","ieee":"E. Sitarska et al., “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41173-1","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 2023;14. doi:10.1038/s41467-023-41173-1"},"article_type":"original","date_published":"2023-09-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2023","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","author":[{"full_name":"Sitarska, Ewa","first_name":"Ewa","last_name":"Sitarska"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"full_name":"Beckwith, Marianne Sandvold","last_name":"Beckwith","first_name":"Marianne Sandvold"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A"},{"full_name":"Czuchnowski, Jakub","first_name":"Jakub","last_name":"Czuchnowski"},{"full_name":"Siggel, Marc","last_name":"Siggel","first_name":"Marc"},{"full_name":"Roessner, Rita","first_name":"Rita","last_name":"Roessner"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"full_name":"Ejsing, Christer","last_name":"Ejsing","first_name":"Christer"},{"full_name":"Schwab, Yannick","first_name":"Yannick","last_name":"Schwab"},{"full_name":"Kosinski, Jan","first_name":"Jan","last_name":"Kosinski"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Kreshuk, Anna","first_name":"Anna","last_name":"Kreshuk"},{"full_name":"Erzberger, Anna","first_name":"Anna","last_name":"Erzberger"},{"last_name":"Diz-Muñoz","first_name":"Alba","full_name":"Diz-Muñoz, Alba"}],"related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-12-21T14:30:01Z","date_created":"2023-09-24T22:01:10Z","volume":14,"article_number":"5644","file_date_updated":"2023-09-25T08:22:58Z","external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"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,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-41173-1","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2041-1723"]}},{"ec_funded":1,"article_number":"adc9584","volume":8,"date_created":"2023-09-06T08:07:51Z","date_updated":"2023-12-21T14:30:01Z","related_material":{"record":[{"id":"14279","status":"public","relation":"research_data"},{"id":"14697","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Alanko, Jonna H","first_name":"Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061"},{"full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"},{"orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","first_name":"Nikola","full_name":"Canigova, Nikola"},{"first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","publication_identifier":{"issn":["2470-9468"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1126/sciimmunol.adc9584","project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"oa":1,"issue":"87","abstract":[{"lang":"eng","text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 8","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14274","article_processing_charge":"No","day":"01","keyword":["General Medicine","Immunology"],"scopus_import":"1","date_published":"2023-09-01T00:00:00Z","article_type":"original","citation":{"mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023."},"publication":"Science Immunology"},{"article_processing_charge":"No","has_accepted_license":"1","day":"20","date_published":"2023-12-20T00:00:00Z","page":"226","citation":{"chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697.","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697"},"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2024-12-20","file_id":"14699","date_updated":"2023-12-20T09:35:34Z","date_created":"2023-12-20T09:35:34Z","checksum":"457927165d5d556305d3086f6b83e5c7","embargo_to":"open_access","file_name":"Thesis.pdf","access_level":"closed","content_type":"application/pdf","file_size":51585778,"creator":"jstopp"},{"relation":"source_file","file_id":"14700","date_updated":"2023-12-20T10:41:42Z","date_created":"2023-12-20T09:35:35Z","checksum":"e8d26449ac461f5e8478a62c9507506f","file_name":"Thesis.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":69625950,"creator":"jstopp"}],"status":"public","ddc":["570"],"title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14697","publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"month":"12","language":[{"iso":"eng"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:14697","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"ec_funded":1,"file_date_updated":"2023-12-20T10:41:42Z","date_updated":"2023-12-21T14:30:02Z","date_created":"2023-12-18T19:14:28Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6328"},{"id":"7885","status":"public","relation":"part_of_dissertation"},{"id":"12272","relation":"part_of_dissertation","status":"public"},{"id":"14274","relation":"part_of_dissertation","status":"public"},{"id":"14360","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publication_status":"published","year":"2023"},{"file_date_updated":"2023-12-14T08:58:18Z","ec_funded":1,"year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11411"}]},"date_updated":"2023-12-22T11:04:45Z","date_created":"2023-12-11T19:30:37Z","month":"12","publication_identifier":{"issn":["2663 - 337X"]},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.15479/at:ista:14651","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"_id":"14651","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","ddc":["570"],"file":[{"file_name":"Phd_Thesis_LA.pdf","access_level":"open_access","creator":"larathoo","content_type":"application/pdf","file_size":34101468,"file_id":"14684","relation":"main_file","date_created":"2023-12-13T15:37:55Z","date_updated":"2023-12-13T15:37:55Z","success":1,"checksum":"520bdb61e95e66070e02824947d2c5fa"},{"file_id":"14685","relation":"source_file","date_created":"2023-12-13T15:42:23Z","date_updated":"2023-12-14T08:58:18Z","checksum":"d8e59afd0817c98fba2564a264508e5c","file_name":"Phd_Thesis_LA.zip","access_level":"closed","creator":"larathoo","content_type":"application/zip","file_size":31052872},{"file_id":"14681","relation":"supplementary_material","checksum":"9a778c949932286f4519e1f1fca2820d","date_created":"2023-12-11T19:24:59Z","date_updated":"2023-12-14T08:58:18Z","access_level":"closed","file_name":"Supplementary_Materials.zip","creator":"larathoo","content_type":"application/zip","file_size":10713896}],"oa_version":"Published Version","day":"12","has_accepted_license":"1","article_processing_charge":"No","citation":{"short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria."},"page":"96","date_published":"2023-12-12T00:00:00Z"},{"abstract":[{"lang":"eng","text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation."}],"article_number":"2312.12213","type":"preprint","author":[{"id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","first_name":"Sadashige","full_name":"Ishida, Sadashige"},{"full_name":"Lavenant, Hugo","first_name":"Hugo","last_name":"Lavenant"}],"date_created":"2023-12-21T10:14:37Z","date_updated":"2023-12-27T13:44:33Z","oa_version":"Preprint","_id":"14703","year":"2023","acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","status":"public","title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"month":"12","day":"19","article_processing_charge":"No","keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"date_published":"2023-12-19T00:00:00Z","doi":"10.48550/arXiv.2312.12213","language":[{"iso":"eng"}],"publication":"arXiv","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.12213","open_access":"1"}],"citation":{"mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213.","short":"S. Ishida, H. Lavenant, ArXiv (n.d.).","chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213.","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213","ista":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213.","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. .","apa":"Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213"},"external_id":{"arxiv":["2312.12213"]},"oa":1,"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}]},{"date_published":"2023-12-01T00:00:00Z","article_type":"original","citation":{"chicago":"Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7.","mla":"Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7.","short":"A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023).","ista":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404.","apa":"Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7","ieee":"A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023.","ama":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7"},"publication":"BMC Microbiology","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"success":1,"checksum":"7ff5e95f3496ff663301eb4a13a316d5","date_updated":"2024-01-02T09:09:32Z","date_created":"2024-01-02T09:09:32Z","file_id":"14723","relation":"main_file","creator":"dernst","file_size":1979922,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_BMCMicrobiology_Yurtseven.pdf"}],"oa_version":"Published Version","intvolume":" 23","status":"public","ddc":["570"],"title":"Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis","_id":"14716","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","abstract":[{"text":"Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1186/s12866-023-03147-7","quality_controlled":"1","external_id":{"pmid":["38124060"]},"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,"publication_identifier":{"eissn":["1471-2180"]},"month":"12","volume":23,"date_updated":"2024-01-02T09:20:57Z","date_created":"2023-12-31T23:01:02Z","author":[{"first_name":"Alper","last_name":"Yurtseven","full_name":"Yurtseven, Alper"},{"last_name":"Buyanova","first_name":"Sofia","id":"2F54A7BC-3902-11EA-AC87-BC9F3DDC885E","full_name":"Buyanova, Sofia"},{"full_name":"Agrawal, Amay Ajaykumar A.","first_name":"Amay Ajaykumar A.","last_name":"Agrawal"},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"last_name":"Kalinina","first_name":"Olga V V.","full_name":"Kalinina, Olga V V."}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B.","file_date_updated":"2024-01-02T09:09:32Z","article_number":"404"},{"ddc":["000"],"title":"Binary decision diagrams on modern hardware","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14718","oa_version":"Published Version","file":[{"date_created":"2024-01-02T08:14:23Z","date_updated":"2024-01-02T08:14:23Z","checksum":"818d6e13dd508f3a04f0941081022e5d","success":1,"relation":"main_file","file_id":"14721","file_size":524321,"content_type":"application/pdf","creator":"dernst","file_name":"2023_FMCAD_Pastva.pdf","access_level":"open_access"}],"type":"conference","abstract":[{"lang":"eng","text":"Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. "}],"page":"122-131","publication":"Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design","citation":{"short":"S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–131.","mla":"Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–31, doi:10.34727/2023/isbn.978-3-85448-060-0_20.","chicago":"Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, 122–31. TU Vienna Academic Press, 2023. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20.","ama":"Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. TU Vienna Academic Press; 2023:122-131. doi:10.34727/2023/isbn.978-3-85448-060-0_20","apa":"Pastva, S., & Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design (pp. 122–131). Ames, IA, United States: TU Vienna Academic Press. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20","ieee":"S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, Ames, IA, United States, 2023, pp. 122–131.","ista":"Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Conference on Formal Methods in Computer-aided design, 122–131."},"date_published":"2023-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"TU Vienna Academic Press","department":[{"_id":"ToHe"}],"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093.","year":"2023","date_updated":"2024-01-02T08:16:28Z","date_created":"2023-12-31T23:01:03Z","author":[{"first_name":"Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"file_date_updated":"2024-01-02T08:14:23Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"oa":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"},"language":[{"iso":"eng"}],"conference":{"start_date":"2023-10-25","location":"Ames, IA, United States","end_date":"2023-10-27","name":"FMCAD: Conference on Formal Methods in Computer-aided design"},"doi":"10.34727/2023/isbn.978-3-85448-060-0_20","month":"10","publication_identifier":{"isbn":["9783854480600"]}},{"date_published":"2023-12-01T00:00:00Z","publication":"Quarterly Journal of Mathematics","citation":{"ista":"Horesh T, Karasik Y. 2023. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 74(4), 1253–1294.","ieee":"T. Horesh and Y. Karasik, “Equidistribution of primitive lattices in ℝn,” Quarterly Journal of Mathematics, vol. 74, no. 4. Oxford University Press, pp. 1253–1294, 2023.","apa":"Horesh, T., & Karasik, Y. (2023). Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haad008","ama":"Horesh T, Karasik Y. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 2023;74(4):1253-1294. doi:10.1093/qmath/haad008","chicago":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics. Oxford University Press, 2023. https://doi.org/10.1093/qmath/haad008.","mla":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics, vol. 74, no. 4, Oxford University Press, 2023, pp. 1253–94, doi:10.1093/qmath/haad008.","short":"T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294."},"article_type":"original","page":"1253-1294","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":724748,"access_level":"open_access","file_name":"2023_QuarterlyJourMath_Horesh.pdf","success":1,"checksum":"bf29baa9eae8500f3374dbcb80712687","date_updated":"2024-01-02T07:37:09Z","date_created":"2024-01-02T07:37:09Z","file_id":"14720","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14717","title":"Equidistribution of primitive lattices in ℝn","ddc":["510"],"status":"public","intvolume":" 74","abstract":[{"text":"We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn, A1, and show that the equidistribution occurs jointly for Λ and A1. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term.","lang":"eng"}],"issue":"4","type":"journal_article","doi":"10.1093/qmath/haad008","language":[{"iso":"eng"}],"oa":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"},"external_id":{"arxiv":["2012.04508"]},"quality_controlled":"1","project":[{"_id":"26A8D266-B435-11E9-9278-68D0E5697425","grant_number":"EP-P026710-2","name":"Between rational and integral points"}],"month":"12","publication_identifier":{"issn":["0033-5606"],"eissn":["1464-3847"]},"author":[{"id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","first_name":"Tal","last_name":"Horesh","full_name":"Horesh, Tal"},{"full_name":"Karasik, Yakov","first_name":"Yakov","last_name":"Karasik"}],"date_created":"2023-12-31T23:01:03Z","date_updated":"2024-01-02T07:39:55Z","volume":74,"acknowledgement":"This work was done when both authors were visiting Institute of Science and Technology (IST) Austria. T.H. was being supported by Engineering and Physical Sciences Research Council grant EP/P026710/1. Y.K. had a great time there and is grateful for the hospitality. The appendix to this paper is largely based on a mini course T.H. had given at IST in February 2020.","year":"2023","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"TiBr"}],"file_date_updated":"2024-01-02T07:37:09Z"},{"abstract":[{"lang":"eng","text":"Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles."}],"issue":"50","type":"journal_article","oa_version":"None","_id":"14719","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","status":"public","intvolume":" 15","day":"05","article_processing_charge":"No","scopus_import":"1","date_published":"2023-12-05T00:00:00Z","publication":"ACS Applied Materials and Interfaces","citation":{"chicago":"Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072.","mla":"Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072.","short":"H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475.","ista":"Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475.","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072","ieee":"H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023.","ama":"Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072"},"article_type":"original","page":"58462–58475","author":[{"last_name":"Mollania","first_name":"Hamid","full_name":"Mollania, Hamid"},{"full_name":"Zhang, Chaoqi","last_name":"Zhang","first_name":"Chaoqi"},{"last_name":"Du","first_name":"Ruifeng","full_name":"Du, Ruifeng"},{"full_name":"Qi, Xueqiang","first_name":"Xueqiang","last_name":"Qi"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","last_name":"Horta"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Keller, Caroline","last_name":"Keller","first_name":"Caroline"},{"full_name":"Chenevier, Pascale","first_name":"Pascale","last_name":"Chenevier"},{"first_name":"Majid","last_name":"Oloomi-Buygi","full_name":"Oloomi-Buygi, Majid"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"date_updated":"2024-01-02T08:35:06Z","date_created":"2023-12-31T23:01:03Z","volume":15,"year":"2023","acknowledgement":"The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF).","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","month":"12","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"doi":"10.1021/acsami.3c14072","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ."}],"issue":"12","type":"journal_article","file":[{"file_size":4346922,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_JourMathPhysics_Mitrouskas.pdf","checksum":"66572f718a36465576cf0d6b3f7e01fc","success":1,"date_created":"2024-01-02T08:45:07Z","date_updated":"2024-01-02T08:45:07Z","relation":"main_file","file_id":"14722"}],"oa_version":"Published Version","status":"public","title":"Exponential decay of the number of excitations in the weakly interacting Bose gas","ddc":["510"],"intvolume":" 64","_id":"14715","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","article_type":"original","publication":"Journal of Mathematical Physics","citation":{"short":"D.J. Mitrouskas, P. Pickl, Journal of Mathematical Physics 64 (2023).","mla":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics, vol. 64, no. 12, 121901, AIP Publishing, 2023, doi:10.1063/5.0172199.","chicago":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0172199.","ama":"Mitrouskas DJ, Pickl P. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 2023;64(12). doi:10.1063/5.0172199","ieee":"D. J. Mitrouskas and P. Pickl, “Exponential decay of the number of excitations in the weakly interacting Bose gas,” Journal of Mathematical Physics, vol. 64, no. 12. AIP Publishing, 2023.","apa":"Mitrouskas, D. J., & Pickl, P. (2023). Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0172199","ista":"Mitrouskas DJ, Pickl P. 2023. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 64(12), 121901."},"file_date_updated":"2024-01-02T08:45:07Z","article_number":"121901","date_updated":"2024-01-02T08:51:28Z","date_created":"2023-12-31T23:01:02Z","volume":64,"author":[{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"year":"2023","acknowledgement":"We thank Lea Boßmann, Phan Thành Nam and Simone Rademacher for helpful remarks. P.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Grant No. SFB/TRR 352 “Mathematics of Many-Body Quantum Systems and Their Collective Phenomena.”","month":"12","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0172199","quality_controlled":"1","oa":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"},"external_id":{"arxiv":["2307.11062"]}},{"file":[{"creator":"sjeschke","file_size":511572575,"content_type":"video/mp4","access_level":"open_access","file_name":"PaperVideo_final.mp4","success":1,"checksum":"1d178bb2f8011d9f5aedda6427e18c7a","date_created":"2023-12-21T12:26:40Z","date_updated":"2023-12-21T12:26:40Z","file_id":"14704","relation":"main_file"},{"date_created":"2024-01-02T09:34:27Z","date_updated":"2024-01-02T09:34:27Z","success":1,"checksum":"a49b2e744d5cd1276bb8b2e0ce6dc638","file_id":"14725","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7469177,"file_name":"2023_ACMToG_Jeschke.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"14240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Generalizing shallow water simulations with dispersive surface waves","ddc":["000"],"intvolume":" 42","abstract":[{"text":"This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a bulk flow (which approximately satisfies the assumptions of the shallow water equations) and surface waves (which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an exact correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2023-08-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"ista":"Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83.","ieee":"S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.","apa":"Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3592098","ama":"Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098","chicago":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592098.","mla":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42, no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023)."},"article_type":"original","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"date_created":"2023-08-27T22:01:17Z","date_updated":"2024-01-02T09:35:55Z","volume":42,"year":"2023","acknowledgement":"We thank Georg Sperl for helping with early research for this paper, Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing Group for general feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat were modeled by Sergei and the palmtrees by YadroGames. The environment map was created by Emil Persson.","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","file_date_updated":"2024-01-02T09:34:27Z","article_number":"83","doi":"10.1145/3592098","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"oa":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"},"external_id":{"isi":["001044671300049"]},"isi":1,"quality_controlled":"1","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"month":"08","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]}},{"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4","ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4","ieee":"A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023).","chicago":"Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4."},"publication":"Nature Communications","date_published":"2023-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells."}],"intvolume":" 14","ddc":["530"],"status":"public","title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14710","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14714","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","success":1,"date_created":"2023-12-27T08:40:43Z","date_updated":"2023-12-27T08:40:43Z","access_level":"open_access","file_name":"2023_NatureComm_Curatolo.pdf","file_size":1342319,"content_type":"application/pdf","creator":"kschuh"}],"publication_identifier":{"eissn":["20411723"]},"month":"12","quality_controlled":"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-43168-4","article_number":"8328","file_date_updated":"2023-12-27T08:40:43Z","department":[{"_id":"CaGo"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).","volume":14,"date_updated":"2024-01-02T11:36:46Z","date_created":"2023-12-24T23:00:53Z","author":[{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"full_name":"Kimchi, Ofer","first_name":"Ofer","last_name":"Kimchi"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"last_name":"Krueger","first_name":"Ryan K.","full_name":"Krueger, Ryan K."},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}]},{"abstract":[{"text":"Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.","lang":"eng"}],"issue":"22","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"f66fb960fd791dea53fd0e087f2fbbe8","success":1,"date_updated":"2024-01-02T09:23:57Z","date_created":"2024-01-02T09:23:57Z","relation":"main_file","file_id":"14724","content_type":"application/pdf","file_size":425194,"creator":"dernst","access_level":"open_access","file_name":"2023_JourExperimentalBotany_DelBianco.pdf"}],"ddc":["580"],"status":"public","title":"Auxin research: Creating tools for a greener future","intvolume":" 74","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14709","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","article_type":"original","page":"6889-6892","publication":"Journal of Experimental Botany","citation":{"chicago":"Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.","short":"M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892.","mla":"Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420.","apa":"Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420","ieee":"M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.","ista":"Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.","ama":"Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420"},"file_date_updated":"2024-01-02T09:23:57Z","date_created":"2023-12-24T23:00:53Z","date_updated":"2024-01-02T09:29:24Z","volume":74,"author":[{"last_name":"Del Bianco","first_name":"Marta","full_name":"Del Bianco, Marta"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Strader, Lucia","first_name":"Lucia","last_name":"Strader"},{"last_name":"Kepinski","first_name":"Stefan","full_name":"Kepinski, Stefan"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","year":"2023","pmid":1,"month":"12","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"language":[{"iso":"eng"}],"doi":"10.1093/jxb/erad420","quality_controlled":"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"},"oa":1,"external_id":{"pmid":["38038239"]}},{"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"month":"12","main_file_link":[{"url":"https://doi.org/10.1093/plcell/koad324","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","doi":"10.1093/plcell/koad324","language":[{"iso":"eng"}],"article_number":"koad324","extern":"1","year":"2023","publisher":"Oxford University Press","publication_status":"epub_ahead","author":[{"last_name":"Zhou","first_name":"Liang-Zi","full_name":"Zhou, Liang-Zi"},{"last_name":"Wang","first_name":"Lele","full_name":"Wang, Lele"},{"first_name":"Xia","last_name":"Chen","full_name":"Chen, Xia"},{"last_name":"Ge","first_name":"Zengxiang","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","full_name":"Ge, Zengxiang"},{"full_name":"Mergner, Julia","last_name":"Mergner","first_name":"Julia"},{"last_name":"Li","first_name":"Xingli","full_name":"Li, Xingli"},{"last_name":"Küster","first_name":"Bernhard","full_name":"Küster, Bernhard"},{"full_name":"Längst, Gernot","last_name":"Längst","first_name":"Gernot"},{"full_name":"Qu, Li-Jia","last_name":"Qu","first_name":"Li-Jia"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"}],"date_created":"2024-01-02T11:19:37Z","date_updated":"2024-01-03T12:43:41Z","keyword":["Cell Biology","Plant Science"],"article_processing_charge":"No","has_accepted_license":"1","day":"23","citation":{"ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324.","ieee":"L.-Z. Zhou et al., “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” The Plant Cell. Oxford University Press, 2023.","apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad324","ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 2023. doi:10.1093/plcell/koad324","chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koad324.","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell, koad324, Oxford University Press, 2023, doi:10.1093/plcell/koad324.","short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023)."},"publication":"The Plant Cell","article_type":"original","date_published":"2023-12-23T00:00:00Z","type":"journal_article","abstract":[{"text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14726","ddc":["580"],"title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","status":"public","oa_version":"Published Version"},{"volume":24,"date_created":"2023-04-16T22:01:08Z","date_updated":"2024-01-04T12:42:09Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7950"}]},"author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"first_name":"Kshitij","last_name":"Jain","full_name":"Jain, Kshitij"},{"full_name":"Lubiw, Anna","first_name":"Anna","last_name":"Lubiw"},{"first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"last_name":"Miltzow","first_name":"Tillmann","full_name":"Miltzow, Tillmann"},{"last_name":"Mondal","first_name":"Debajyoti","full_name":"Mondal, Debajyoti"},{"first_name":"Anurag Murty","last_name":"Naredla","full_name":"Naredla, Anurag Murty"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"last_name":"Turcotte","first_name":"Alexi","full_name":"Turcotte, Alexi"}],"department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"UlWa"}],"publisher":"EPI Sciences","publication_status":"published","year":"2023","acknowledgement":"This work was begun at the University of Waterloo and was partially supported by the Natural Sciences and Engineering Council of Canada (NSERC).\r\n","file_date_updated":"2023-04-17T08:10:28Z","article_number":"9","language":[{"iso":"eng"}],"doi":"10.46298/DMTCS.8383","quality_controlled":"1","oa":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"},"external_id":{"arxiv":["1903.06981"]},"publication_identifier":{"issn":["1462-7264"],"eissn":["1365-8050"]},"month":"01","file":[{"date_updated":"2023-04-17T08:10:28Z","date_created":"2023-04-17T08:10:28Z","checksum":"439102ea4f6e2aeefd7107dfb9ccf532","success":1,"relation":"main_file","file_id":"12844","content_type":"application/pdf","file_size":2072197,"creator":"dernst","file_name":"2022_DMTCS_Biniaz.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 24","ddc":["000"],"status":"public","title":"Token swapping on trees","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"12833","issue":"2","abstract":[{"lang":"eng","text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved."}],"type":"journal_article","date_published":"2023-01-18T00:00:00Z","article_type":"original","citation":{"short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, Discrete Mathematics and Theoretical Computer Science 24 (2023).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2, 9, EPI Sciences, 2023, doi:10.46298/DMTCS.8383.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science. EPI Sciences, 2023. https://doi.org/10.46298/DMTCS.8383.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 2023;24(2). doi:10.46298/DMTCS.8383","ieee":"A. Biniaz et al., “Token swapping on trees,” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2. EPI Sciences, 2023.","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (2023). Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. EPI Sciences. https://doi.org/10.46298/DMTCS.8383","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. 2023. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 24(2), 9."},"publication":"Discrete Mathematics and Theoretical Computer Science","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1"},{"page":"3-20","publication":"27th International Conference on Financial Cryptography and Data Security","citation":{"mla":"Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1.","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1.","ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1","ista":"Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","apa":"Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1"},"date_published":"2023-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Executing and proving over dirty ledgers","status":"public","intvolume":" 13950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14735","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs."}],"quality_controlled":"1","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1554"}],"language":[{"iso":"eng"}],"conference":{"name":"FC: Financial Cryptography and Data Security","location":"Bol, Brac, Croatia","start_date":"2023-05-01","end_date":"2023-05-05"},"doi":"10.1007/978-3-031-47754-6_1","month":"12","publication_identifier":{"eissn":["0302-9743"],"isbn":["9783031477539"],"issn":["1611-3349"],"eisbn":["9783031477546"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ElKo"},{"_id":"GradSch"}],"acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.","year":"2023","date_created":"2024-01-08T09:17:38Z","date_updated":"2024-01-08T09:28:14Z","volume":13950,"author":[{"id":"a20e8902-32b0-11ee-9fa8-b23fa638b793","first_name":"Christos","last_name":"Stefo","full_name":"Stefo, Christos"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"}]},{"author":[{"full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356"},{"full_name":"Hey, Dominic","first_name":"Dominic","last_name":"Hey"},{"full_name":"Kerber, Rachel N.","last_name":"Kerber","first_name":"Rachel N."},{"full_name":"Bond, Andrew D.","last_name":"Bond","first_name":"Andrew D."},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."},{"first_name":"Clare P.","last_name":"Grey","full_name":"Grey, Clare P."}],"date_created":"2024-01-05T09:20:48Z","date_updated":"2024-01-08T09:03:01Z","year":"2023","publication_status":"epub_ahead","publisher":"American Chemical Society","department":[{"_id":"StFr"}],"ec_funded":1,"doi":"10.1021/acsaem.3c02223","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1021/acsaem.3c02223","open_access":"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"},"oa":1,"quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"month":"12","publication_identifier":{"eissn":["2574-0962"]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14733","status":"public","ddc":["540"],"title":"Exploring the landscape of heterocyclic quinones for redox flow batteries","abstract":[{"text":"Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy.","lang":"eng"}],"type":"journal_article","date_published":"2023-12-28T00:00:00Z","publication":"ACS Applied Energy Materials","citation":{"ama":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 2023. doi:10.1021/acsaem.3c02223","ista":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2023. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials.","apa":"Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., & Grey, C. P. (2023). Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02223","ieee":"R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” ACS Applied Energy Materials. American Chemical Society, 2023.","mla":"Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials, American Chemical Society, 2023, doi:10.1021/acsaem.3c02223.","short":"R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials (2023).","chicago":"Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaem.3c02223."},"article_type":"original","day":"28","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","keyword":["Electrical and Electronic Engineering","Materials Chemistry","Electrochemistry","Energy Engineering and Power Technology","Chemical Engineering (miscellaneous)"]},{"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_type":"original","quality_controlled":"1","citation":{"mla":"Wan, Shanhong, et al. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods, Wiley, 2023, doi:10.1002/smtd.202301377.","short":"S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023).","chicago":"Wan, Shanhong, Shanshan Xiao, Mingquan Li, Xin Wang, Khak Ho Lim, Min Hong, Maria Ibáñez, Andreu Cabot, and Yu Liu. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods. Wiley, 2023. https://doi.org/10.1002/smtd.202301377.","ama":"Wan S, Xiao S, Li M, et al. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. 2023. doi:10.1002/smtd.202301377","ista":"Wan S, Xiao S, Li M, Wang X, Lim KH, Hong M, Ibáñez M, Cabot A, Liu Y. 2023. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods.","apa":"Wan, S., Xiao, S., Li, M., Wang, X., Lim, K. H., Hong, M., … Liu, Y. (2023). Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. Wiley. https://doi.org/10.1002/smtd.202301377","ieee":"S. Wan et al., “Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4,” Small Methods. Wiley, 2023."},"external_id":{"pmid":["38152986"]},"publication":"Small Methods","language":[{"iso":"eng"}],"date_published":"2023-12-28T00:00:00Z","doi":"10.1002/smtd.202301377","scopus_import":"1","publication_identifier":{"eissn":["2366-9608"]},"article_processing_charge":"No","day":"28","month":"12","publisher":"Wiley","department":[{"_id":"MaIb"}],"publication_status":"epub_ahead","status":"public","title":"Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4","pmid":1,"_id":"14734","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","year":"2023","oa_version":"None","date_updated":"2024-01-08T09:17:04Z","date_created":"2024-01-07T23:00:51Z","author":[{"last_name":"Wan","first_name":"Shanhong","full_name":"Wan, Shanhong"},{"full_name":"Xiao, Shanshan","last_name":"Xiao","first_name":"Shanshan"},{"full_name":"Li, Mingquan","first_name":"Mingquan","last_name":"Li"},{"full_name":"Wang, Xin","last_name":"Wang","first_name":"Xin"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"first_name":"Min","last_name":"Hong","full_name":"Hong, Min"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu","last_name":"Liu"}],"type":"journal_article","abstract":[{"text":"Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology.","lang":"eng"}]},{"file_date_updated":"2024-01-08T09:53:09Z","volume":2023,"date_updated":"2024-01-08T09:57:25Z","date_created":"2024-01-08T09:48:56Z","author":[{"first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"last_name":"Naszódi","first_name":"Márton","full_name":"Naszódi, Márton"}],"publisher":"Oxford University Press","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"We thank Alexander Litvak for the many discussions on Theorem 1.1. Igor Tsiutsiurupa participated in the early stage of this project. To our deep regret, Igor chose another road for his life and stopped working with us.\r\nThis work was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences [to M.N.]; the National Research, Development, and Innovation Fund (NRDI) [K119670 and K131529 to M.N.]; and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the NRDI [to M.N.].","year":"2023","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnad210","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2212.11781"]},"issue":"23","abstract":[{"lang":"eng","text":"John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies."}],"type":"journal_article","file":[{"file_size":815777,"content_type":"application/pdf","creator":"dernst","file_name":"2023_IMRN_Ivanov.pdf","access_level":"open_access","date_updated":"2024-01-08T09:53:09Z","date_created":"2024-01-08T09:53:09Z","checksum":"353666cea80633beb0f1ffd342dff6d4","success":1,"relation":"main_file","file_id":"14738"}],"oa_version":"Published Version","intvolume":" 2023","title":"Functional John and Löwner conditions for pairs of log-concave functions","ddc":["510"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14737","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","keyword":["General Mathematics"],"date_published":"2023-12-01T00:00:00Z","page":"20613-20669","article_type":"original","citation":{"ista":"Ivanov G, Naszódi M. 2023. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023(23), 20613–20669.","apa":"Ivanov, G., & Naszódi, M. (2023). Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnad210","ieee":"G. Ivanov and M. Naszódi, “Functional John and Löwner conditions for pairs of log-concave functions,” International Mathematics Research Notices, vol. 2023, no. 23. Oxford University Press, pp. 20613–20669, 2023.","ama":"Ivanov G, Naszódi M. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023;2023(23):20613-20669. doi:10.1093/imrn/rnad210","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices. Oxford University Press, 2023. https://doi.org/10.1093/imrn/rnad210.","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices, vol. 2023, no. 23, Oxford University Press, 2023, pp. 20613–69, doi:10.1093/imrn/rnad210.","short":"G. Ivanov, M. Naszódi, International Mathematics Research Notices 2023 (2023) 20613–20669."},"publication":"International Mathematics Research Notices"},{"article_processing_charge":"No","day":"01","page":"309-325","citation":{"ama":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. R2: Boosting liquidity in payment channel networks with online admission control. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:309-325. doi:10.1007/978-3-031-47754-6_18","apa":"Bastankhah, M., Chatterjee, K., Maddah-Ali, M. A., Schmid, S., Svoboda, J., & Yeo, M. X. (2023). R2: Boosting liquidity in payment channel networks with online admission control. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 309–325). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_18","ieee":"M. Bastankhah, K. Chatterjee, M. A. Maddah-Ali, S. Schmid, J. Svoboda, and M. X. Yeo, “R2: Boosting liquidity in payment channel networks with online admission control,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 309–325.","ista":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. 2023. R2: Boosting liquidity in payment channel networks with online admission control. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 309–325.","short":"M. Bastankhah, K. Chatterjee, M.A. Maddah-Ali, S. Schmid, J. Svoboda, M.X. Yeo, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 309–325.","mla":"Bastankhah, Mahsa, et al. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 309–25, doi:10.1007/978-3-031-47754-6_18.","chicago":"Bastankhah, Mahsa, Krishnendu Chatterjee, Mohammad Ali Maddah-Ali, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” In 27th International Conference on Financial Cryptography and Data Security, 13950:309–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_18."},"publication":"27th International Conference on Financial Cryptography and Data Security","date_published":"2023-12-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks.","lang":"eng"}],"intvolume":" 13950","status":"public","title":"R2: Boosting liquidity in payment channel networks with online admission control","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14736","oa_version":"None","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031477539"],"issn":["0302-9743"],"eisbn":["9783031477546"]},"month":"12","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-47754-6_18","conference":{"location":"Bol, Brac, Croatia","start_date":"2023-05-01","end_date":"2023-05-05","name":"FC: Financial Cryptography and Data Security"},"ec_funded":1,"publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"KrPi"}],"publication_status":"published","acknowledgement":"Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt).","year":"2023","volume":13950,"date_created":"2024-01-08T09:30:22Z","date_updated":"2024-01-08T09:36:36Z","author":[{"full_name":"Bastankhah, Mahsa","last_name":"Bastankhah","first_name":"Mahsa"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Mohammad Ali","last_name":"Maddah-Ali","full_name":"Maddah-Ali, Mohammad Ali"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","first_name":"Michelle X"}]},{"abstract":[{"lang":"eng","text":"Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods."}],"issue":"12","type":"journal_article","file":[{"file_id":"14740","relation":"main_file","success":1,"checksum":"465c28ef0b151b4b1fb47977ed5581ab","date_updated":"2024-01-08T10:09:14Z","date_created":"2024-01-08T10:09:14Z","access_level":"open_access","file_name":"2023_IEEEToP_Ali.pdf","creator":"dernst","file_size":2370988,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["000"],"status":"public","title":"A survey of vectorization methods in topological data analysis","intvolume":" 45","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14739","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["Applied Mathematics","Artificial Intelligence","Computational Theory and Mathematics","Computer Vision and Pattern Recognition","Software"],"date_published":"2023-12-01T00:00:00Z","article_type":"original","page":"14069-14080","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"ama":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391","ista":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080.","apa":"Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391","ieee":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023.","mla":"Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391.","short":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080.","chicago":"Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391."},"file_date_updated":"2024-01-08T10:09:14Z","date_updated":"2024-01-08T10:11:46Z","date_created":"2024-01-08T09:59:46Z","volume":45,"author":[{"full_name":"Ali, Dashti","last_name":"Ali","first_name":"Dashti"},{"full_name":"Asaad, Aras","first_name":"Aras","last_name":"Asaad"},{"full_name":"Jimenez, Maria-Jose","first_name":"Maria-Jose","last_name":"Jimenez"},{"full_name":"Nanda, Vidit","first_name":"Vidit","last_name":"Nanda"},{"full_name":"Paluzo-Hidalgo, Eduardo","first_name":"Eduardo","last_name":"Paluzo-Hidalgo"},{"orcid":"0000-0003-2449-1433","id":"15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8","last_name":"Soriano Trigueros","first_name":"Manuel","full_name":"Soriano Trigueros, Manuel"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"HeEd"}],"acknowledgement":"The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions.","year":"2023","month":"12","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"language":[{"iso":"eng"}],"doi":"10.1109/tpami.2023.3308391","quality_controlled":"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"},"oa":1},{"month":"11","publication_identifier":{"issn":["1943-0264"]},"quality_controlled":"1","external_id":{"pmid":["37604585"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/cshperspect.a041447","article_number":"a041447","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Cold Spring Harbor Laboratory","year":"2023","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","pmid":1,"date_updated":"2024-01-08T12:52:29Z","date_created":"2024-01-08T12:43:48Z","volume":15,"author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"full_name":"Giménez, Mabel D.","last_name":"Giménez","first_name":"Mabel D."},{"first_name":"Mathieu","last_name":"Joron","full_name":"Joron, Mathieu"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"full_name":"Searle, Jeremy B.","last_name":"Searle","first_name":"Jeremy B."},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Cold Spring Harbor Perspectives in Biology","citation":{"ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447","ieee":"K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447."},"date_published":"2023-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"issue":"11","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","status":"public","intvolume":" 15","_id":"14742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.\r\nUsing our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties.","lang":"eng"}],"title":"Divide & Scale: Formalization and roadmap to robust sharding","status":"public","intvolume":" 13892","_id":"14744","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","page":"199-245","publication":"30th International Colloquium on Structural Information and Communication Complexity","citation":{"chicago":"Avarikioti, Zeta, Antoine Desjardins, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” In 30th International Colloquium on Structural Information and Communication Complexity, 13892:199–245. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_10.","mla":"Avarikioti, Zeta, et al. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” 30th International Colloquium on Structural Information and Communication Complexity, vol. 13892, Springer Nature, 2023, pp. 199–245, doi:10.1007/978-3-031-32733-9_10.","short":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, R. Wattenhofer, in:, 30th International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2023, pp. 199–245.","ista":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. 2023. Divide & Scale: Formalization and roadmap to robust sharding. 30th International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 199–245.","ieee":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, and R. Wattenhofer, “Divide & Scale: Formalization and roadmap to robust sharding,” in 30th International Colloquium on Structural Information and Communication Complexity, Alcalá de Henares, Spain, 2023, vol. 13892, pp. 199–245.","apa":"Avarikioti, Z., Desjardins, A., Kokoris Kogias, E., & Wattenhofer, R. (2023). Divide & Scale: Formalization and roadmap to robust sharding. In 30th International Colloquium on Structural Information and Communication Complexity (Vol. 13892, pp. 199–245). Alcalá de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_10","ama":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. Divide & Scale: Formalization and roadmap to robust sharding. In: 30th International Colloquium on Structural Information and Communication Complexity. Vol 13892. Springer Nature; 2023:199-245. doi:10.1007/978-3-031-32733-9_10"},"date_published":"2023-06-01T00:00:00Z","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388).","year":"2023","date_created":"2024-01-08T12:56:46Z","date_updated":"2024-01-09T07:40:57Z","volume":13892,"author":[{"first_name":"Zeta","last_name":"Avarikioti","full_name":"Avarikioti, Zeta"},{"id":"06d0c166-aec1-11ee-a7c0-b96e840a602b","first_name":"Antoine","last_name":"Desjardins","full_name":"Desjardins, Antoine"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Wattenhofer","first_name":"Roger","full_name":"Wattenhofer, Roger"}],"month":"06","publication_identifier":{"eisbn":["9783031327339"],"issn":["0302-9743"],"isbn":["9783031327322"],"eissn":["1611-3349"]},"quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"location":"Alcalá de Henares, Spain","start_date":"2023-06-06","end_date":"2023-06-09","name":"SIROCCO: Structural Information and Communication Complexity"},"doi":"10.1007/978-3-031-32733-9_10"},{"day":"21","article_processing_charge":"No","scopus_import":"1","keyword":["Atomic and Molecular Physics","and Optics"],"date_published":"2023-07-21T00:00:00Z","publication":"Optics Letters","citation":{"chicago":"Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofya Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters. Optica Publishing Group, 2023. https://doi.org/10.1364/ol.495553.","short":"U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976.","mla":"Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:10.1364/ol.495553.","ieee":"U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” Optics Letters, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023.","apa":"Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., & Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/ol.495553","ista":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976.","ama":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 2023;48(15):3973-3976. doi:10.1364/ol.495553"},"article_type":"original","page":"3973-3976","abstract":[{"text":"We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry.","lang":"eng"}],"issue":"15","type":"journal_article","oa_version":"Preprint","_id":"14749","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Monitoring and active stabilization of laser injection locking using beam ellipticity","status":"public","intvolume":" 48","month":"07","publication_identifier":{"eissn":["1539-4794"],"issn":["0146-9592"]},"doi":"10.1364/ol.495553","language":[{"iso":"eng"}],"external_id":{"arxiv":["2212.01266"]},"quality_controlled":"1","author":[{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang","last_name":"Mishra","full_name":"Mishra, Umang"},{"last_name":"Li","first_name":"Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Vyacheslav"},{"full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald"},{"full_name":"Agafonova, Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","orcid":"0000-0003-0582-2946","first_name":"Sofya","last_name":"Agafonova"},{"id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico","first_name":"Fritz R","full_name":"Diorico, Fritz R"},{"orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur"}],"date_updated":"2024-01-09T08:09:32Z","date_created":"2024-01-08T13:01:46Z","volume":48,"year":"2023","publication_status":"published","publisher":"Optica Publishing Group","department":[{"_id":"OnHo"}]},{"date_published":"2023-06-01T00:00:00Z","publication":"AGU Advances","citation":{"chicago":"Fildier, B., Caroline J Muller, R. Pincus, and S. Fueglistaler. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances. American Geophysical Union, 2023. https://doi.org/10.1029/2023av000880.","mla":"Fildier, B., et al. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances, vol. 4, no. 3, e2023AV000880, American Geophysical Union, 2023, doi:10.1029/2023av000880.","short":"B. Fildier, C.J. Muller, R. Pincus, S. Fueglistaler, AGU Advances 4 (2023).","ista":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. 2023. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 4(3), e2023AV000880.","ieee":"B. Fildier, C. J. Muller, R. Pincus, and S. Fueglistaler, “How moisture shapes low‐level radiative cooling in subsidence regimes,” AGU Advances, vol. 4, no. 3. American Geophysical Union, 2023.","apa":"Fildier, B., Muller, C. J., Pincus, R., & Fueglistaler, S. (2023). How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. American Geophysical Union. https://doi.org/10.1029/2023av000880","ama":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 2023;4(3). doi:10.1029/2023av000880"},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","keyword":["General Earth and Planetary Sciences"],"file":[{"file_id":"14761","relation":"main_file","date_created":"2024-01-09T08:51:25Z","date_updated":"2024-01-09T08:51:25Z","success":1,"checksum":"af773220a9fa194c61a8dc2fae092c16","file_name":"2023_AGUAdvances_Fildier.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":24149551}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14752","status":"public","ddc":["550"],"title":"How moisture shapes low‐level radiative cooling in subsidence regimes","intvolume":" 4","abstract":[{"lang":"eng","text":"Radiative cooling of the lowest atmospheric levels is of strong importance for modulating atmospheric circulations and organizing convection, but detailed observations and a robust theoretical understanding are lacking. Here we use unprecedented observational constraints from subsidence regimes in the tropical Atlantic to develop a theory for the shape and magnitude of low‐level longwave radiative cooling in clear‐sky, showing peaks larger than 5–10 K/day at the top of the boundary layer. A suite of novel scaling approximations is first developed from simplified spectral theory, in close agreement with the measurements. The radiative cooling peak height is set by the maximum lapse rate in water vapor path, and its magnitude is mainly controlled by the ratio of column relative humidity above and below the peak. We emphasize how elevated intrusions of moist air can reduce low‐level cooling, by sporadically shading the spectral range which effectively cools to space. The efficiency of this spectral shading depends both on water content and altitude of moist intrusions; its height dependence cannot be explained by the temperature difference between the emitting and absorbing layers, but by the decrease of water vapor extinction with altitude. This analytical work can help to narrow the search for low‐level cloud patterns sensitive to radiative‐convective feedbacks: the most organized patterns with largest cloud fractions occur in atmospheres below 10% relative humidity and feel the strongest low‐level cooling. This motivates further assessment of favorable conditions for radiative‐convective feedbacks and a robust quantification of corresponding shallow cloud dynamics in current and warmer climates."}],"issue":"3","type":"journal_article","doi":"10.1029/2023av000880","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"month":"06","publication_identifier":{"eissn":["2576-604X"]},"author":[{"full_name":"Fildier, B.","first_name":"B.","last_name":"Fildier"},{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"Pincus, R.","last_name":"Pincus","first_name":"R."},{"full_name":"Fueglistaler, S.","first_name":"S.","last_name":"Fueglistaler"}],"date_created":"2024-01-08T13:07:49Z","date_updated":"2024-01-09T08:54:03Z","volume":4,"acknowledgement":"The authors would like to thank two anonymous reviews and gratefully acknowledge diverse funding agencies and resources used for this work. B.F. and C.M. thank funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041), and the EUREC4A campaign organizers for giving the opportunity to take part to the campaign and use the data early on. R. P. was supported by the US National Science Foundation (award AGS 19–16908), by the National Oceanic and Atmospheric Administration (award NA200AR4310375), and the Vetlesen Foundation.","year":"2023","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"American Geophysical Union","file_date_updated":"2024-01-09T08:51:25Z","ec_funded":1,"article_number":"e2023AV000880"},{"file_date_updated":"2024-01-09T09:13:53Z","article_number":"0112","author":[{"last_name":"Wang","first_name":"B.","full_name":"Wang, B."},{"last_name":"Mellibovsky","first_name":"F.","full_name":"Mellibovsky, F."},{"full_name":"Ayats López, Roger","first_name":"Roger","last_name":"Ayats López","id":"ab77522d-073b-11ed-8aff-e71b39258362","orcid":"0000-0001-6572-0621"},{"full_name":"Deguchi, K.","last_name":"Deguchi","first_name":"K."},{"full_name":"Meseguer, A.","first_name":"A.","last_name":"Meseguer"}],"date_created":"2024-01-08T13:11:45Z","date_updated":"2024-01-09T09:15:29Z","volume":381,"acknowledgement":"K.D.’s research was supported by Australian Research Council Discovery Early Career Researcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitividad (grant nos. FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant no. PID2020-114043GB-I00) and the Generalitat de Catalunya (grant no. 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152). F.M. is a Serra-Húnter Fellow.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"The Royal Society","month":"05","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"doi":"10.1098/rsta.2022.0112","language":[{"iso":"eng"}],"external_id":{"pmid":["36907214"]},"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,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role."}],"issue":"2246","type":"journal_article","file":[{"date_created":"2024-01-09T09:13:53Z","date_updated":"2024-01-09T09:13:53Z","success":1,"checksum":"1978d126c0ce2f47c22ac20107cc0106","file_id":"14763","relation":"main_file","creator":"dernst","file_size":6421086,"content_type":"application/pdf","file_name":"2023_PhilTransactionsA_Wang_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"14754","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mean structure of the supercritical turbulent spiral in Taylor–Couette flow","status":"public","ddc":["530"],"intvolume":" 381","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["General Physics and Astronomy","General Engineering","General Mathematics"],"date_published":"2023-05-01T00:00:00Z","publication":"Philosophical Transactions of the Royal Society A","citation":{"ama":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 2023;381(2246). doi:10.1098/rsta.2022.0112","ista":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. 2023. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 381(2246), 0112.","ieee":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, and A. Meseguer, “Mean structure of the supercritical turbulent spiral in Taylor–Couette flow,” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246. The Royal Society, 2023.","apa":"Wang, B., Mellibovsky, F., Ayats López, R., Deguchi, K., & Meseguer, A. (2023). Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. The Royal Society. https://doi.org/10.1098/rsta.2022.0112","mla":"Wang, B., et al. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246, 0112, The Royal Society, 2023, doi:10.1098/rsta.2022.0112.","short":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023).","chicago":"Wang, B., F. Mellibovsky, Roger Ayats López, K. Deguchi, and A. Meseguer. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A. The Royal Society, 2023. https://doi.org/10.1098/rsta.2022.0112."},"article_type":"original"},{"publication":"Physics Letters B","citation":{"apa":"Faccioli, P., Krätschmer, I., & Lourenço, C. (2023). Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2023.137871","ieee":"P. Faccioli, I. Krätschmer, and C. Lourenço, “Low-pT quarkonium polarization measurements: Challenges and opportunities,” Physics Letters B, vol. 840. Elsevier, 2023.","ista":"Faccioli P, Krätschmer I, Lourenço C. 2023. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 840, 137871.","ama":"Faccioli P, Krätschmer I, Lourenço C. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 2023;840. doi:10.1016/j.physletb.2023.137871","chicago":"Faccioli, Pietro, Ilse Krätschmer, and Carlos Lourenço. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B. Elsevier, 2023. https://doi.org/10.1016/j.physletb.2023.137871.","short":"P. Faccioli, I. Krätschmer, C. Lourenço, Physics Letters B 840 (2023).","mla":"Faccioli, Pietro, et al. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B, vol. 840, 137871, Elsevier, 2023, doi:10.1016/j.physletb.2023.137871."},"article_type":"original","date_published":"2023-05-10T00:00:00Z","scopus_import":"1","keyword":["Nuclear and High Energy Physics"],"day":"10","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","_id":"14753","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["530"],"title":"Low-pT quarkonium polarization measurements: Challenges and opportunities","intvolume":" 840","file":[{"file_name":"2023_PhysicsLettersB_Faccioli.pdf","access_level":"open_access","file_size":855494,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14762","date_created":"2024-01-09T08:59:24Z","date_updated":"2024-01-09T08:59:24Z","checksum":"02dec160dbc81d95985e755869d8afbf","success":1}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT\r\n quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion.","lang":"eng"}],"oa":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"},"quality_controlled":"1","doi":"10.1016/j.physletb.2023.137871","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1873-2445"],"issn":["0370-2693"]},"year":"2023","acknowledgement":"P.F. and C.L. acknowledge support from Fundação para a Ciência e a Tecnologia, Portugal, under contract CERN/FIS-PAR/0010/2019.\r\nOpen Access funded by SCOAP3.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaRo"}],"author":[{"last_name":"Faccioli","first_name":"Pietro","full_name":"Faccioli, Pietro"},{"full_name":"Krätschmer, Ilse","last_name":"Krätschmer","first_name":"Ilse","orcid":"0000-0002-5636-9259","id":"30d4014e-7753-11eb-b44b-db6d61112e73"},{"full_name":"Lourenço, Carlos","first_name":"Carlos","last_name":"Lourenço"}],"date_created":"2024-01-08T13:09:17Z","date_updated":"2024-01-09T09:02:22Z","volume":840,"article_number":"137871","file_date_updated":"2024-01-09T08:59:24Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14750","intvolume":" 33","status":"public","title":"Local laws for multiplication of random matrices","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"Consider the random matrix model A1/2UBU∗A1/2, where A and B are two N × N deterministic matrices and U is either an N × N Haar unitary or orthogonal random matrix. It is well known that on the macroscopic scale (Invent. Math. 104 (1991) 201–220), the limiting empirical spectral distribution (ESD) of the above model is given by the free multiplicative convolution\r\nof the limiting ESDs of A and B, denoted as μα \u0002 μβ, where μα and μβ are the limiting ESDs of A and B, respectively. In this paper, we study the asymptotic microscopic behavior of the edge eigenvalues and eigenvectors statistics. We prove that both the density of μA \u0002μB, where μA and μB are the ESDs of A and B, respectively and the associated subordination functions\r\nhave a regular behavior near the edges. Moreover, we establish the local laws near the edges on the optimal scale. In particular, we prove that the entries of the resolvent are close to some functionals depending only on the eigenvalues of A, B and the subordination functions with optimal convergence rates. Our proofs and calculations are based on the techniques developed for the additive model A+UBU∗ in (J. Funct. Anal. 271 (2016) 672–719; Comm. Math.\r\nPhys. 349 (2017) 947–990; Adv. Math. 319 (2017) 251–291; J. Funct. Anal. 279 (2020) 108639), and our results can be regarded as the counterparts of (J. Funct. Anal. 279 (2020) 108639) for the multiplicative model. ","lang":"eng"}],"citation":{"ista":"Ding X, Ji HC. 2023. Local laws for multiplication of random matrices. The Annals of Applied Probability. 33(4), 2981–3009.","ieee":"X. Ding and H. C. Ji, “Local laws for multiplication of random matrices,” The Annals of Applied Probability, vol. 33, no. 4. Institute of Mathematical Statistics, pp. 2981–3009, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Local laws for multiplication of random matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1882","ama":"Ding X, Ji HC. Local laws for multiplication of random matrices. The Annals of Applied Probability. 2023;33(4):2981-3009. doi:10.1214/22-aap1882","chicago":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1882.","mla":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability, vol. 33, no. 4, Institute of Mathematical Statistics, 2023, pp. 2981–3009, doi:10.1214/22-aap1882.","short":"X. Ding, H.C. Ji, The Annals of Applied Probability 33 (2023) 2981–3009."},"publication":"The Annals of Applied Probability","page":"2981-3009","article_type":"original","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"article_processing_charge":"No","day":"01","acknowledgement":"The first author is partially supported by NSF Grant DMS-2113489 and grateful for the AMS-SIMONS travel grant (2020–2023). The second author is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors would like to thank the Editor, Associate Editor and an anonymous referee for their many critical suggestions which have significantly improved the paper. We also want to thank Zhigang Bao and Ji Oon Lee for many helpful discussions and comments.","year":"2023","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"last_name":"Ding","first_name":"Xiucai","full_name":"Ding, Xiucai"},{"full_name":"Ji, Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang","last_name":"Ji"}],"volume":33,"date_created":"2024-01-08T13:03:18Z","date_updated":"2024-01-09T08:16:41Z","ec_funded":1,"oa":1,"external_id":{"arxiv":["2010.16083"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2010.16083","open_access":"1"}],"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1214/22-aap1882","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1050-5164"]},"month":"08"},{"issue":"3","abstract":[{"lang":"eng","text":"We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.\r\nTo construct examples, we explicitly describe Spin 2r-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category."}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":707344,"creator":"dernst","file_name":"2023_QuantumTopol_Carqueville.pdf","access_level":"open_access","date_created":"2024-01-09T09:25:34Z","date_updated":"2024-01-09T09:25:34Z","checksum":"b0590aff6e7ec89cc149ba94d459d3a3","success":1,"relation":"main_file","file_id":"14764"}],"oa_version":"Published Version","intvolume":" 14","title":"Fully extended r-spin TQFTs","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14756","has_accepted_license":"1","article_processing_charge":"Yes","day":"16","keyword":["Geometry and Topology","Mathematical Physics"],"scopus_import":"1","date_published":"2023-10-16T00:00:00Z","page":"467-532","article_type":"original","citation":{"mla":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology, vol. 14, no. 3, European Mathematical Society, 2023, pp. 467–532, doi:10.4171/qt/193.","short":"N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532.","chicago":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology. European Mathematical Society, 2023. https://doi.org/10.4171/qt/193.","ama":"Carqueville N, Szegedy L. Fully extended r-spin TQFTs. Quantum Topology. 2023;14(3):467-532. doi:10.4171/qt/193","ista":"Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 467–532.","apa":"Carqueville, N., & Szegedy, L. (2023). Fully extended r-spin TQFTs. Quantum Topology. European Mathematical Society. https://doi.org/10.4171/qt/193","ieee":"N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” Quantum Topology, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023."},"publication":"Quantum Topology","file_date_updated":"2024-01-09T09:25:34Z","volume":14,"date_updated":"2024-01-09T09:27:46Z","date_created":"2024-01-08T13:14:48Z","author":[{"last_name":"Carqueville","first_name":"Nils","full_name":"Carqueville, Nils"},{"full_name":"Szegedy, Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","orcid":"0000-0003-2834-5054","first_name":"Lorant","last_name":"Szegedy"}],"publisher":"European Mathematical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"N.C. is supported by the DFG Heisenberg Programme.\r\nWe are grateful to Tobias Dyckerhoff, Lukas Müller, Ingo Runkel, and Christopher Schommer-Pries for helpful discussions.","year":"2023","publication_identifier":{"issn":["1663-487X"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.4171/qt/193","quality_controlled":"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"},"oa":1},{"author":[{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan","last_name":"Zhang","full_name":"Zhang, Yihan"}],"volume":69,"date_created":"2024-01-08T13:04:54Z","date_updated":"2024-01-09T08:45:24Z","acknowledgement":"The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]","year":"2023","department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"month":"07","doi":"10.1109/tit.2023.3257239","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2101.12426"}],"external_id":{"arxiv":["2101.12426"]},"oa":1,"quality_controlled":"1","issue":"7","abstract":[{"lang":"eng","text":"We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation."}],"type":"journal_article","oa_version":"Preprint","_id":"14751","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 69","status":"public","title":"Zero-error communication over adversarial MACs","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Computer Science Applications","Information Systems"],"date_published":"2023-07-01T00:00:00Z","citation":{"chicago":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/tit.2023.3257239.","mla":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory, vol. 69, no. 7, Institute of Electrical and Electronics Engineers, 2023, pp. 4093–127, doi:10.1109/tit.2023.3257239.","short":"Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127.","ista":"Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127.","ieee":"Y. Zhang, “Zero-error communication over adversarial MACs,” IEEE Transactions on Information Theory, vol. 69, no. 7. Institute of Electrical and Electronics Engineers, pp. 4093–4127, 2023.","apa":"Zhang, Y. (2023). Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2023.3257239","ama":"Zhang Y. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 2023;69(7):4093-4127. doi:10.1109/tit.2023.3257239"},"publication":"IEEE Transactions on Information Theory","page":"4093-4127","article_type":"original"},{"oa_version":"Preprint","_id":"14755","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 131","title":"Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result","status":"public","issue":"3-4","abstract":[{"lang":"eng","text":"We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T > 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021))."}],"type":"journal_article","date_published":"2023-02-02T00:00:00Z","citation":{"chicago":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis. IOS Press, 2023. https://doi.org/10.3233/asy-221775.","mla":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis, vol. 131, no. 3–4, IOS Press, 2023, pp. 297–383, doi:10.3233/asy-221775.","short":"M. Moser, Asymptotic Analysis 131 (2023) 297–383.","ista":"Moser M. 2023. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 131(3–4), 297–383.","apa":"Moser, M. (2023). Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. IOS Press. https://doi.org/10.3233/asy-221775","ieee":"M. Moser, “Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result,” Asymptotic Analysis, vol. 131, no. 3–4. IOS Press, pp. 297–383, 2023.","ama":"Moser M. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 2023;131(3-4):297-383. doi:10.3233/asy-221775"},"publication":"Asymptotic Analysis","page":"297-383","article_type":"original","article_processing_charge":"No","day":"02","scopus_import":"1","keyword":["General Mathematics"],"author":[{"last_name":"Moser","first_name":"Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","full_name":"Moser, Maximilian"}],"volume":131,"date_created":"2024-01-08T13:13:28Z","date_updated":"2024-01-09T09:22:16Z","acknowledgement":"The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work.","year":"2023","publisher":"IOS Press","department":[{"_id":"JuFi"}],"publication_status":"published","doi":"10.3233/asy-221775","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.07100"}],"external_id":{"arxiv":["2105.07100"]},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["0921-7134"],"eissn":["1875-8576"]},"month":"02"},{"abstract":[{"text":"The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression.","lang":"eng"}],"type":"book_chapter","author":[{"orcid":"0000-0002-5615-5277","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","last_name":"Villalba Requena","first_name":"Ana","full_name":"Villalba Requena, Ana"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"oa_version":"None","date_updated":"2024-01-09T09:46:57Z","date_created":"2024-01-08T13:16:36Z","_id":"14757","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","department":[{"_id":"SiHi"}],"editor":[{"full_name":"Huttner, Wieland","first_name":"Wieland","last_name":"Huttner"}],"publication_status":"published","status":"public","title":"Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression","article_processing_charge":"No","publication_identifier":{"eisbn":["9781119860914"]},"month":"08","day":"08","scopus_import":"1","doi":"10.1002/9781119860914.ch10","date_published":"2023-08-08T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10","apa":"Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10","ieee":"A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression,” in Neocortical Neurogenesis in Development and Evolution, W. Huttner, Ed. Wiley, 2023, pp. 169–191.","ista":"Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.","short":"A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191.","mla":"Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10.","chicago":"Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10."},"publication":"Neocortical Neurogenesis in Development and Evolution","page":"169-191","quality_controlled":"1"},{"quality_controlled":"1","external_id":{"arxiv":["2208.11591"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.11591","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1364/ao.474118","publication_identifier":{"issn":["1559-128X"],"eissn":["2155-3165"]},"month":"01","publisher":"Optica Publishing Group","department":[{"_id":"OnHo"}],"publication_status":"published","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","year":"2023","volume":62,"date_updated":"2024-01-09T10:10:34Z","date_created":"2024-01-08T13:19:14Z","author":[{"first_name":"Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","orcid":"0000-0002-5869-1604","full_name":"Wald, Sebastian"},{"last_name":"Diorico","first_name":"Fritz R","orcid":"0000-0002-4947-8924","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","full_name":"Diorico, Fritz R"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur"}],"page":"1-7","article_type":"original","citation":{"chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics. Optica Publishing Group, 2023. https://doi.org/10.1364/ao.474118.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:10.1364/ao.474118.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","apa":"Wald, S., Diorico, F. R., & Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. Optica Publishing Group. https://doi.org/10.1364/ao.474118","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” Applied Optics, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 2023;62(1):1-7. doi:10.1364/ao.474118"},"publication":"Applied Optics","date_published":"2023-01-01T00:00:00Z","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 62","status":"public","title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","_id":"14759","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method."}]},{"status":"public","ddc":["570"],"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12817","year":"2023","acknowledgement":"We thank J. 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. 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N. "},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"last_name":"Pfister","first_name":"Hanspeter"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"type":"research_data","license":"https://creativecommons.org/licenses/by-sa/4.0/","abstract":[{"lang":"eng","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."}],"file_date_updated":"2023-05-18T19:51:52Z","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","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"},"citation":{"chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817.","mla":"Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817.","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, 10.15479/AT:ISTA:12817.","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817","ama":"Danzl JG. 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Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous 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 a 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"}],"type":"journal_article","oa_version":"Published Version","title":"Dense 4D nanoscale reconstruction of living brain tissue","status":"public","intvolume":" 20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13267","day":"01","article_processing_charge":"Yes","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","page":"1256-1265","publication":"Nature Methods","citation":{"ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6."},"ec_funded":1,"date_created":"2023-07-23T22:01:13Z","date_updated":"2024-01-10T08:37:48Z","volume":20,"author":[{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431"},{"last_name":"Miguel Villalba","first_name":"Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder"},{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"first_name":"Donglai","last_name":"Wei","full_name":"Wei, Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","first_name":"Jake","last_name":"Watson"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"full_name":"Beyer, Johanna","last_name":"Beyer","first_name":"Johanna"},{"first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G.N.","last_name":"Grant","first_name":"Seth G.N."},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"12817","relation":"research_data","status":"public"},{"id":"14770","status":"public","relation":"shorter_version"}],"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"year":"2023","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","pmid":1,"month":"08","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41592-023-01936-6","isi":1,"quality_controlled":"1","project":[{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"main_file_link":[{"url":"https://doi.org/10.1038/s41592-023-01936-6","open_access":"1"}],"oa":1},{"date_created":"2024-01-10T08:42:40Z","date_updated":"2024-01-10T08:59:26Z","related_material":{"link":[{"url":"https://github.com/IST-DASLab/pruned-vision-model-bias","relation":"software"}]},"author":[{"first_name":"Eugenia B","last_name":"Iofinova","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B"},{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"publisher":"IEEE","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"published","acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","year":"2023","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1109/cvpr52729.2023.02334","conference":{"end_date":"2023-06-24","start_date":"2023-06-17","location":"Vancouver, BC, Canada","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"project":[{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":" W1260-N35"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2304.12622"],"isi":["001062531308068"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.12622","open_access":"1"}],"publication_identifier":{"eisbn":["9798350301298"],"eissn":["2575-7075"]},"month":"08","oa_version":"Preprint","status":"public","title":"Bias in pruned vision models: In-depth analysis and countermeasures","_id":"14771","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.","lang":"eng"}],"type":"conference","date_published":"2023-08-22T00:00:00Z","page":"24364-24373","citation":{"mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–73, doi:10.1109/cvpr52729.2023.02334.","short":"E.B. Iofinova, E.-A. Peste, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24364–73. IEEE, 2023. https://doi.org/10.1109/cvpr52729.2023.02334.","ama":"Iofinova EB, Peste E-A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2023:24364-24373. doi:10.1109/cvpr52729.2023.02334","ista":"Iofinova EB, Peste E-A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","ieee":"E. B. Iofinova, E.-A. Peste, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Vancouver, BC, Canada, 2023, pp. 24364–24373.","apa":"Iofinova, E. B., Peste, E.-A., & Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24364–24373). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/cvpr52729.2023.02334"},"publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","article_processing_charge":"No","day":"22"},{"quality_controlled":"1","isi":1,"external_id":{"isi":["001025621500002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41592-023-01937-5","month":"08","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"year":"2023","date_created":"2024-01-10T08:07:15Z","date_updated":"2024-01-10T08:37:48Z","volume":20,"author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"13267","status":"public","relation":"extended_version"}]},"article_type":"letter_note","page":"1141-1142","publication":"Nature Methods","citation":{"ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5."},"date_published":"2023-08-01T00:00:00Z","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","intvolume":" 20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14770","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"issue":"8"},{"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"AnKi"}],"year":"2023","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","pmid":1,"date_updated":"2024-01-10T12:45:25Z","date_created":"2024-01-10T09:18:54Z","volume":150,"author":[{"last_name":"Harish","first_name":"Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","full_name":"Harish, Rohit K"},{"full_name":"Gupta, Mansi","last_name":"Gupta","first_name":"Mansi"},{"full_name":"Zöller, Daniela","last_name":"Zöller","first_name":"Daniela"},{"first_name":"Hella","last_name":"Hartmann","full_name":"Hartmann, Hella"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"last_name":"Machate","first_name":"Anja","full_name":"Machate, Anja"},{"full_name":"Hans, Stefan","first_name":"Stefan","last_name":"Hans"},{"first_name":"Michael","last_name":"Brand","full_name":"Brand, Michael"}],"article_number":"dev201559","file_date_updated":"2024-01-10T12:41:13Z","isi":1,"quality_controlled":"1","external_id":{"isi":["001097449100002"],"pmid":["37665167"]},"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,"language":[{"iso":"eng"}],"doi":"10.1242/dev.201559","month":"10","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","ddc":["570"],"status":"public","intvolume":" 150","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14774","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":12836306,"access_level":"open_access","file_name":"2023_Development_Harish.pdf","success":1,"checksum":"2d6f52dc33260a9b2352b8f28374ba5f","date_created":"2024-01-10T12:41:13Z","date_updated":"2024-01-10T12:41:13Z","file_id":"14790","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"issue":"19","article_type":"original","publication":"Development","citation":{"chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development. The Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:10.1242/dev.201559.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","ieee":"R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” Development, vol. 150, no. 19. The Company of Biologists, 2023.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. The Company of Biologists. https://doi.org/10.1242/dev.201559","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 2023;150(19). doi:10.1242/dev.201559"},"date_published":"2023-10-01T00:00:00Z","keyword":["Developmental Biology","Molecular Biology"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"publication_identifier":{"issn":["1422-0067"]},"month":"11","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"},"external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3390/ijms242216527","language":[{"iso":"eng"}],"article_number":"16527","file_date_updated":"2024-01-10T13:39:42Z","pmid":1,"acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","year":"2023","publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","last_name":"Teplova"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"full_name":"Serebryakova, Marina V.","first_name":"Marina V.","last_name":"Serebryakova"},{"full_name":"Golyshev, Sergei A.","last_name":"Golyshev","first_name":"Sergei A."},{"first_name":"Raisa A.","last_name":"Galiullina","full_name":"Galiullina, Raisa A."},{"full_name":"Chichkova, Nina V.","last_name":"Chichkova","first_name":"Nina V."},{"full_name":"Vartapetian, Andrey B.","first_name":"Andrey B.","last_name":"Vartapetian"}],"volume":24,"date_updated":"2024-01-10T13:41:10Z","date_created":"2024-01-10T09:24:35Z","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"01","citation":{"ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","ieee":"A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” International Journal of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms242216527.","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023)."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2023-11-01T00:00:00Z","type":"journal_article","issue":"22","abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"_id":"14776","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","ddc":["580"],"status":"public","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2637784,"file_name":"2023_IJMS_Teplova.pdf","access_level":"open_access","date_updated":"2024-01-10T13:39:42Z","date_created":"2024-01-10T13:39:42Z","success":1,"checksum":"4df7d206ba022b7f54eff1f0aec1659a","file_id":"14791","relation":"main_file"}]},{"month":"02","publication_identifier":{"issn":["1050-5164"]},"isi":1,"quality_controlled":"1","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"oa":1,"external_id":{"isi":["000946432400021"],"arxiv":["2108.02728"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.02728","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1214/22-aap1826","ec_funded":1,"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2023","acknowledgement":"K. Schnelli was supported by the Swedish Research Council Grants VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","date_created":"2024-01-10T09:23:31Z","date_updated":"2024-01-10T13:31:46Z","volume":33,"author":[{"full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli"},{"full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","last_name":"Xu","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","orcid":"0000-0003-1559-1205"}],"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"677-725","publication":"The Annals of Applied Probability","citation":{"chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1826.","short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725.","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 677–725, doi:10.1214/22-aap1826.","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices,” The Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023.","apa":"Schnelli, K., & Xu, Y. (2023). Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1826","ista":"Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1), 677–725.","ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 2023;33(1):677-725. doi:10.1214/22-aap1826"},"date_published":"2023-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble."}],"issue":"1","status":"public","title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","intvolume":" 33","_id":"14775","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"AIP Publishing","year":"2023","date_updated":"2024-01-10T12:38:02Z","date_created":"2024-01-10T09:18:04Z","volume":76,"author":[{"full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350"},{"first_name":"Sophie","last_name":"Abramian","full_name":"Abramian, Sophie"}],"article_number":"28","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf","open_access":"1"}],"oa":1,"external_id":{"isi":["000984516100007"]},"language":[{"iso":"eng"}],"doi":"10.1063/pt.3.5234","month":"05","publication_identifier":{"issn":["0031-9228"],"eissn":["1945-0699"]},"status":"public","title":"The cloud dynamics of convective storm systems","intvolume":" 76","_id":"14773","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics."}],"issue":"5","article_type":"original","publication":"Physics Today","citation":{"ama":"Muller CJ, Abramian S. The cloud dynamics of convective storm systems. Physics Today. 2023;76(5). doi:10.1063/pt.3.5234","ista":"Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28.","ieee":"C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” Physics Today, vol. 76, no. 5. AIP Publishing, 2023.","apa":"Muller, C. J., & Abramian, S. (2023). The cloud dynamics of convective storm systems. Physics Today. AIP Publishing. https://doi.org/10.1063/pt.3.5234","mla":"Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today, vol. 76, no. 5, 28, AIP Publishing, 2023, doi:10.1063/pt.3.5234.","short":"C.J. Muller, S. Abramian, Physics Today 76 (2023).","chicago":"Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today. AIP Publishing, 2023. https://doi.org/10.1063/pt.3.5234."},"date_published":"2023-05-01T00:00:00Z","keyword":["General Physics and Astronomy"],"day":"01","article_processing_charge":"No"},{"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["General Physics and Astronomy"],"date_published":"2023-12-01T00:00:00Z","publication":"AIP Advances","citation":{"ieee":"K. Sato et al., “Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” AIP Advances, vol. 13, no. 12. AIP Publishing, 2023.","apa":"Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M., & Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. AIP Publishing. https://doi.org/10.1063/5.0171888","ista":"Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.","ama":"Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 2023;13(12). doi:10.1063/5.0171888","chicago":"Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances. AIP Publishing, 2023. https://doi.org/10.1063/5.0171888.","short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023).","mla":"Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances, vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:10.1063/5.0171888."},"article_type":"original","abstract":[{"text":"The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators.","lang":"eng"}],"issue":"12","type":"journal_article","file":[{"file_name":"2023_AIPAdvances_Sato.pdf","access_level":"open_access","file_size":9676071,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14792","date_updated":"2024-01-10T13:47:31Z","date_created":"2024-01-10T13:47:31Z","checksum":"a7098388b8ff822b47f5ddd37ed3bdbc","success":1}],"oa_version":"Published Version","_id":"14777","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","ddc":["540"],"intvolume":" 13","month":"12","publication_identifier":{"eissn":["2158-3226"]},"doi":"10.1063/5.0171888","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"},"external_id":{"isi":["001114917200005"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2024-01-10T13:47:31Z","article_number":"125206","author":[{"full_name":"Sato, Kosuke","first_name":"Kosuke","last_name":"Sato"},{"full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","first_name":"Saurabh","last_name":"Singh"},{"last_name":"Yamazaki","first_name":"Itsuki","full_name":"Yamazaki, Itsuki"},{"last_name":"Hirata","first_name":"Keisuke","full_name":"Hirata, Keisuke"},{"full_name":"Ang, Artoni Kevin R.","first_name":"Artoni Kevin R.","last_name":"Ang"},{"full_name":"Matsunami, Masaharu","first_name":"Masaharu","last_name":"Matsunami"},{"last_name":"Takeuchi","first_name":"Tsunehiro","full_name":"Takeuchi, Tsunehiro"}],"date_updated":"2024-01-10T13:49:09Z","date_created":"2024-01-10T09:26:08Z","volume":13,"acknowledgement":"This work received financial support partially from Japan Science and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology Foundation, Aichi, Japan (Proposal No. 202301057).","year":"2023","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"AIP Publishing"},{"date_published":"2023-11-17T00:00:00Z","publication":"Geometriae Dedicata","citation":{"chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2023. https://doi.org/10.1007/s10711-023-00862-3.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature, 2023, doi:10.1007/s10711-023-00862-3.","apa":"Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata. Springer Nature, 2023.","ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3"},"article_type":"original","day":"17","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","_id":"9651","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Divergence of separated nets with respect to displacement equivalence","status":"public","abstract":[{"text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.","lang":"eng"}],"type":"journal_article","doi":"10.1007/s10711-023-00862-3","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s10711-023-00862-3","open_access":"1"}],"oa":1,"external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"]},"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"author":[{"first_name":"Michael","last_name":"Dymond","full_name":"Dymond, Michael"},{"full_name":"Kaluza, Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698","first_name":"Vojtech","last_name":"Kaluza"}],"date_updated":"2024-01-11T13:06:32Z","date_created":"2021-07-14T07:01:27Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","year":"2023","publication_status":"epub_ahead","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","article_number":"15"},{"page":"1105-1130","publication":"2023 IEEE 64th Annual Symposium on Foundations of Computer Science","citation":{"short":"V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.","mla":"Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–30, doi:10.1109/focs57990.2023.00066.","chicago":"Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, 1105–30. IEEE, 2023. https://doi.org/10.1109/focs57990.2023.00066.","ama":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high dimensional spaces: Sketches and approximation. In: 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. IEEE; 2023:1105-1130. doi:10.1109/focs57990.2023.00066","apa":"Cohen-Addad, V., Saulpic, D., & Schwiegelshohn, C. (2023). Deterministic clustering in high dimensional spaces: Sketches and approximation. In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science (pp. 1105–1130). Santa Cruz, CA, United States: IEEE. https://doi.org/10.1109/focs57990.2023.00066","ieee":"V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering in high dimensional spaces: Sketches and approximation,” in 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, Santa Cruz, CA, United States, 2023, pp. 1105–1130.","ista":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 1105–1130."},"date_published":"2023-12-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","title":"Deterministic clustering in high dimensional spaces: Sketches and approximation","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14768","oa_version":"Preprint","type":"conference","abstract":[{"text":"In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\\varepsilon^{-O(1)} \\log k$ dimensions in time $k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$, and how to build a coreset of size $O\\left(k^{2} \\log ^{3} k \\varepsilon^{-O(1)}\\right)$ in time $2^{\\varepsilon^{O(1)} k \\log ^{3} k}+k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \\log ^{3} k / \\varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \\varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.","lang":"eng"}],"quality_controlled":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"}],"external_id":{"arxiv":["2310.04076"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.04076","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"FOCS: Symposium on Foundations of Computer Science","end_date":"2023-11-09","start_date":"2023-11-06","location":"Santa Cruz, CA, United States"},"doi":"10.1109/focs57990.2023.00066","month":"12","publication_identifier":{"eisbn":["9798350318944"]},"publication_status":"published","publisher":"IEEE","department":[{"_id":"MoHe"}],"year":"2023","acknowledgement":"D. Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader grant No 1051-00106B.","date_created":"2024-01-09T16:20:09Z","date_updated":"2024-01-16T07:28:06Z","author":[{"first_name":"Vincent","last_name":"Cohen-Addad","full_name":"Cohen-Addad, Vincent"},{"last_name":"Saulpic","first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David"},{"full_name":"Schwiegelshohn, Chris","first_name":"Chris","last_name":"Schwiegelshohn"}],"ec_funded":1},{"article_number":"adg1610","file_date_updated":"2024-01-16T09:35:28Z","year":"2023","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FlSc"}],"author":[{"full_name":"Gallardo-Dodd, Carlos J.","first_name":"Carlos J.","last_name":"Gallardo-Dodd"},{"last_name":"Oertlin","first_name":"Christian","full_name":"Oertlin, Christian"},{"full_name":"Record, Julien","last_name":"Record","first_name":"Julien"},{"last_name":"Galvani","first_name":"Rômulo G.","full_name":"Galvani, Rômulo G."},{"full_name":"Sommerauer, Christian","last_name":"Sommerauer","first_name":"Christian"},{"first_name":"Nikolai V.","last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai V."},{"full_name":"Doukoumopoulos, Evangelos","first_name":"Evangelos","last_name":"Doukoumopoulos"},{"full_name":"Ali, Liaqat","last_name":"Ali","first_name":"Liaqat"},{"first_name":"Mariana M. S.","last_name":"Oliveira","full_name":"Oliveira, Mariana M. S."},{"full_name":"Seitz, Christina","last_name":"Seitz","first_name":"Christina"},{"full_name":"Percipalle, Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","first_name":"Mathias","last_name":"Percipalle"},{"first_name":"Tijana","last_name":"Nikić","full_name":"Nikić, Tijana"},{"last_name":"Sadova","first_name":"Anastasia A.","full_name":"Sadova, Anastasia A."},{"full_name":"Shulgina, Sofia M.","last_name":"Shulgina","first_name":"Sofia M."},{"full_name":"Shmarov, Vjacheslav A.","first_name":"Vjacheslav A.","last_name":"Shmarov"},{"full_name":"Kutko, Olga V.","last_name":"Kutko","first_name":"Olga V."},{"full_name":"Vlasova, Daria D.","last_name":"Vlasova","first_name":"Daria D."},{"last_name":"Orlova","first_name":"Kseniya D.","full_name":"Orlova, Kseniya D."},{"last_name":"Rykova","first_name":"Marina P.","full_name":"Rykova, Marina P."},{"first_name":"John","last_name":"Andersson","full_name":"Andersson, John"},{"full_name":"Percipalle, Piergiorgio","last_name":"Percipalle","first_name":"Piergiorgio"},{"full_name":"Kutter, Claudia","last_name":"Kutter","first_name":"Claudia"},{"full_name":"Ponomarev, Sergey A.","last_name":"Ponomarev","first_name":"Sergey A."},{"first_name":"Lisa S.","last_name":"Westerberg","full_name":"Westerberg, Lisa S."}],"date_updated":"2024-01-16T09:38:58Z","date_created":"2024-01-10T09:48:01Z","volume":9,"month":"08","publication_identifier":{"issn":["2375-2548"]},"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"},"external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1126/sciadv.adg1610","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.","lang":"eng"}],"issue":"34","_id":"14784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","intvolume":" 9","oa_version":"Published Version","file":[{"file_name":"2023_ScienceAdvances_GallardoDodd.pdf","access_level":"open_access","file_size":1596639,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14809","date_created":"2024-01-16T09:35:28Z","date_updated":"2024-01-16T09:35:28Z","checksum":"b9072e20e2d5d9d34d2c53319bafee41","success":1}],"keyword":["Multidisciplinary"],"day":"25","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Science Advances","citation":{"ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","ieee":"C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” Science Advances, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg1610","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023)."},"article_type":"original","date_published":"2023-08-25T00:00:00Z"},{"file_date_updated":"2024-01-16T09:09:29Z","author":[{"first_name":"Lucia","last_name":"Baldauf","full_name":"Baldauf, Lucia"},{"full_name":"Frey, Felix F","first_name":"Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Marcos","last_name":"Arribas Perez","full_name":"Arribas Perez, Marcos"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."}],"related_material":{"link":[{"relation":"software","url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing"}]},"date_updated":"2024-01-16T09:20:03Z","date_created":"2024-01-10T09:45:48Z","volume":122,"acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","year":"2023","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"AnSa"}],"month":"06","publication_identifier":{"issn":["0006-3495"]},"doi":"10.1016/j.bpj.2023.02.018","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["36806830"],"isi":["001016792600001"]},"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration."}],"issue":"11","type":"journal_article","file":[{"file_id":"14807","relation":"main_file","success":1,"checksum":"70566e54cd95ea6df340909ad44c5cd5","date_updated":"2024-01-16T09:09:29Z","date_created":"2024-01-16T09:09:29Z","access_level":"open_access","file_name":"2023_BiophysicalJournal_Baldauf.pdf","creator":"dernst","content_type":"application/pdf","file_size":3285810}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14782","ddc":["570"],"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","status":"public","intvolume":" 122","day":"06","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","keyword":["Biophysics"],"date_published":"2023-06-06T00:00:00Z","publication":"Biophysical Journal","citation":{"chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018"},"article_type":"original","page":"2311-2324"},{"issue":"8","abstract":[{"lang":"eng","text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy."}],"type":"journal_article","file":[{"file_id":"14808","relation":"main_file","success":1,"checksum":"6798cd75d8857976fbc58a43fd173d68","date_created":"2024-01-16T09:26:52Z","date_updated":"2024-01-16T09:26:52Z","access_level":"open_access","file_name":"2023_Cells_Cheung.pdf","creator":"dernst","content_type":"application/pdf","file_size":7931643}],"oa_version":"Published Version","intvolume":" 12","ddc":["570"],"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14783","has_accepted_license":"1","article_processing_charge":"Yes","day":"11","keyword":["General Medicine"],"date_published":"2023-04-11T00:00:00Z","article_type":"original","citation":{"ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133","ieee":"G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023, doi:10.3390/cells12081133.","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12081133."},"publication":"Cells","file_date_updated":"2024-01-16T09:26:52Z","article_number":"1133","volume":12,"date_updated":"2024-01-16T09:29:35Z","date_created":"2024-01-10T09:46:35Z","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"full_name":"Chever, Oana","last_name":"Chever","first_name":"Oana"},{"last_name":"Rollenhagen","first_name":"Astrid","full_name":"Rollenhagen, Astrid"},{"first_name":"Nicole","last_name":"Quenech’du","full_name":"Quenech’du, Nicole"},{"last_name":"Ezan","first_name":"Pascal","full_name":"Ezan, Pascal"},{"last_name":"Lübke","first_name":"Joachim H. R.","full_name":"Lübke, Joachim H. R."},{"full_name":"Rouach, Nathalie","first_name":"Nathalie","last_name":"Rouach"}],"publisher":"MDPI","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","publication_identifier":{"issn":["2073-4409"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.3390/cells12081133","quality_controlled":"1","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"},"external_id":{"isi":["000977445700001"],"pmid":["37190042"]},"oa":1},{"issue":"6","abstract":[{"text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2023_EnvirMicroBiolReports_Nies.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1518350,"file_id":"14810","relation":"main_file","date_updated":"2024-01-16T09:42:10Z","date_created":"2024-01-16T09:42:10Z","success":1,"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3"}],"oa_version":"Published Version","intvolume":" 15","title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","status":"public","ddc":["570"],"_id":"14785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-12-01T00:00:00Z","page":"656-668","article_type":"original","citation":{"mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., & Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.13203","ieee":"F. Nies et al., “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023."},"publication":"Environmental Microbiology Reports","file_date_updated":"2024-01-16T09:42:10Z","volume":15,"date_updated":"2024-01-16T09:46:12Z","date_created":"2024-01-10T10:41:07Z","author":[{"first_name":"Fabian","last_name":"Nies","full_name":"Nies, Fabian"},{"first_name":"Tanita","last_name":"Wein","full_name":"Wein, Tanita"},{"full_name":"Hanke, Dustin M.","first_name":"Dustin M.","last_name":"Hanke"},{"full_name":"Springstein, Benjamin L","first_name":"Benjamin L","last_name":"Springstein","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","orcid":"0000-0002-3461-5391"},{"first_name":"Jaime","last_name":"Alcorta","full_name":"Alcorta, Jaime"},{"last_name":"Taubenheim","first_name":"Claudia","full_name":"Taubenheim, Claudia"},{"full_name":"Dagan, Tal","first_name":"Tal","last_name":"Dagan"}],"publisher":"Wiley","department":[{"_id":"MaLo"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","publication_identifier":{"eissn":["1758-2229"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1111/1758-2229.13203","quality_controlled":"1","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"},"oa":1,"external_id":{"pmid":["37794696"],"isi":["001080203100001"]}},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"date_published":"2023-09-01T00:00:00Z","article_type":"original","page":"25-60","publication":"Stochastic Processes and their Applications","citation":{"short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications, vol. 163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.","chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications. Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009.","ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” Stochastic Processes and their Applications, vol. 163. Elsevier, pp. 25–60, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2023.05.009","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60."},"abstract":[{"text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1870349,"file_name":"2023_StochasticProcAppl_Ding.pdf","access_level":"open_access","date_updated":"2024-01-16T08:47:31Z","date_created":"2024-01-16T08:47:31Z","success":1,"checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","file_id":"14806","relation":"main_file"}],"oa_version":"Published Version","status":"public","ddc":["510"],"title":"Spiked multiplicative random matrices and principal components","intvolume":" 163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14780","month":"09","publication_identifier":{"eissn":["1879-209X"],"issn":["0304-4149"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.spa.2023.05.009","isi":1,"quality_controlled":"1","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"oa":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"},"external_id":{"isi":["001113615900001"],"arxiv":["2302.13502"]},"file_date_updated":"2024-01-16T08:47:31Z","ec_funded":1,"date_created":"2024-01-10T09:29:25Z","date_updated":"2024-01-16T08:49:51Z","volume":163,"author":[{"last_name":"Ding","first_name":"Xiucai","full_name":"Ding, Xiucai"},{"full_name":"Ji, Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","last_name":"Ji","first_name":"Hong Chang"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"LaEr"}],"acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","year":"2023"},{"article_type":"original","citation":{"short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:10.1029/2023gl103043.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters. American Geophysical Union, 2023. https://doi.org/10.1029/2023gl103043.","ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 2023;50(11). doi:10.1029/2023gl103043","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” Geophysical Research Letters, vol. 50, no. 11. American Geophysical Union, 2023.","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., & Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl103043","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043."},"publication":"Geophysical Research Letters","date_published":"2023-06-16T00:00:00Z","keyword":["General Earth and Planetary Sciences","Geophysics"],"has_accepted_license":"1","article_processing_charge":"No","day":"16","intvolume":" 50","title":"The decaying near‐surface boundary layer of a retreating alpine glacier","ddc":["550"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14779","oa_version":"Published Version","file":[{"file_size":2529327,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","checksum":"391a3005c95340a0ae129ce4fbdf2bae","success":1,"date_created":"2024-01-16T08:35:02Z","date_updated":"2024-01-16T08:35:02Z","relation":"main_file","file_id":"14805"}],"type":"journal_article","issue":"11","abstract":[{"text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers.","lang":"eng"}],"quality_controlled":"1","isi":1,"oa":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"},"external_id":{"isi":["000999436400001"]},"language":[{"iso":"eng"}],"doi":"10.1029/2023gl103043","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"month":"06","department":[{"_id":"FrPe"}],"publisher":"American Geophysical Union","publication_status":"published","acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","year":"2023","volume":50,"date_created":"2024-01-10T09:28:34Z","date_updated":"2024-01-16T08:42:36Z","author":[{"full_name":"Shaw, Thomas E.","first_name":"Thomas E.","last_name":"Shaw"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"full_name":"McCarthy, Michael","last_name":"McCarthy","first_name":"Michael"},{"full_name":"Miles, Evan S.","last_name":"Miles","first_name":"Evan S."},{"last_name":"Ayala","first_name":"Álvaro","full_name":"Ayala, Álvaro"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"}],"article_number":"e2023GL103043","file_date_updated":"2024-01-16T08:35:02Z"},{"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","status":"public","intvolume":" 58","_id":"14781","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"issue":"17","article_type":"original","page":"1578-1592.e5","publication":"Developmental Cell","citation":{"chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009"},"date_published":"2023-09-11T00:00:00Z","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"day":"11","article_processing_charge":"No","publication_status":"published","publisher":"Elsevier","department":[{"_id":"Bio"}],"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","year":"2023","pmid":1,"date_updated":"2024-01-16T08:56:36Z","date_created":"2024-01-10T09:41:21Z","volume":58,"author":[{"full_name":"Westerich, Kim Joana","last_name":"Westerich","first_name":"Kim Joana"},{"last_name":"Tarbashevich","first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna"},{"full_name":"Schick, Jan","first_name":"Jan","last_name":"Schick"},{"last_name":"Gupta","first_name":"Antra","full_name":"Gupta, Antra"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"first_name":"Kenneth","last_name":"Hull","full_name":"Hull, Kenneth"},{"last_name":"Romo","first_name":"Daniel","full_name":"Romo, Daniel"},{"first_name":"Dagmar","last_name":"Zeuschner","full_name":"Zeuschner, Dagmar"},{"full_name":"Goudarzi, Mohammad","last_name":"Goudarzi","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gross-Thebing, Theresa","first_name":"Theresa","last_name":"Gross-Thebing"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"quality_controlled":"1","external_id":{"pmid":["37463577"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2023.06.009","month":"09","publication_identifier":{"issn":["1534-5807"]}}]