[{"department":[{"_id":"MaLo"}],"file_date_updated":"2023-08-14T07:57:55Z","date_updated":"2023-12-13T12:09:20Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14039","issue":"15","volume":58,"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","file":[{"date_created":"2023-08-14T07:57:55Z","file_name":"2023_DevelopmentalCell_Leonard.pdf","creator":"dernst","date_updated":"2023-08-14T07:57:55Z","file_size":3184217,"file_id":"14049","checksum":"d8c5dc97cd40c26da2ec98ae723ab368","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 58","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"}],"oa_version":"Published Version","pmid":1,"author":[{"full_name":"Leonard, Thomas A.","last_name":"Leonard","first_name":"Thomas A."},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"full_name":"Martens, Sascha","last_name":"Martens","first_name":"Sascha"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37419118"],"isi":["001059110400001"]},"title":"The membrane surface as a platform that organizes cellular and biochemical processes","citation":{"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.","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","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","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"},{"_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","name":"Synthetic and structural biology of Rab GTPase networks","grant_number":"101045340"}],"page":"1315-1332","date_published":"2023-08-07T00:00:00Z","doi":"10.1016/j.devcel.2023.06.001","date_created":"2023-08-13T22:01:12Z","isi":1,"has_accepted_license":"1","year":"2023","day":"07","publication":"Developmental Cell","quality_controlled":"1","publisher":"Elsevier","oa":1,"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."},{"language":[{"iso":"eng"}],"file":[{"file_name":"2023_NatureComm_Zhao.pdf","date_created":"2023-08-14T07:01:12Z","file_size":2315325,"date_updated":"2023-08-14T07:01:12Z","creator":"dernst","success":1,"checksum":"3b9043df3d51c300f9be95eac3ff9d0b","file_id":"14044","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"volume":14,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","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."}],"intvolume":" 14","month":"08","scopus_import":"1","ddc":["570"],"date_updated":"2023-12-13T12:06:56Z","file_date_updated":"2023-08-14T07:01:12Z","department":[{"_id":"LeSa"}],"_id":"14040","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Nature Communications","day":"04","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-08-13T22:01:13Z","doi":"10.1038/s41467-023-40388-6","date_published":"2023-08-04T00:00:00Z","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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (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","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","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."},"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","external_id":{"isi":["001042606700004"]},"article_processing_charge":"Yes","author":[{"full_name":"Zhao, Ziyu","last_name":"Zhao","first_name":"Ziyu"},{"first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino"},{"first_name":"Jana","full_name":"Knoppová, Jana","last_name":"Knoppová"},{"first_name":"Roman","last_name":"Sobotka","full_name":"Sobotka, Roman"},{"first_name":"James W.","full_name":"Murray, James W.","last_name":"Murray"},{"full_name":"Nixon, Peter J.","last_name":"Nixon","first_name":"Peter J."},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Komenda","full_name":"Komenda, Josef","first_name":"Josef"}],"article_number":"4681"},{"type":"conference","conference":{"name":"LICS: Symposium on Logic in Computer Science","location":"Boston, MA, United States","end_date":"2023-06-29","start_date":"2023-06-26"},"status":"public","_id":"13967","department":[{"_id":"KrCh"}],"date_updated":"2023-12-13T12:06:10Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.09930"}],"month":"07","intvolume":" 2023","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"}],"oa_version":"Preprint","volume":2023,"publication_identifier":{"issn":["1043-6871"],"isbn":["9798350335873"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"id":"02ab0197-cc70-11ed-ab61-918e71f56881","first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"}],"article_processing_charge":"No","external_id":{"isi":["001036707700042"],"arxiv":["2304.09930"]},"title":"Stopping criteria for value iteration on stochastic games with quantitative objectives","citation":{"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.","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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","oa":1,"acknowledgement":"This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”.","date_published":"2023-07-01T00:00:00Z","doi":"10.1109/LICS56636.2023.10175771","date_created":"2023-08-06T22:01:10Z","isi":1,"year":"2023","day":"01","publication":"38th Annual ACM/IEEE Symposium on Logic in Computer Science"},{"department":[{"_id":"DaZi"}],"file_date_updated":"2023-08-07T08:32:26Z","date_updated":"2023-12-13T12:05:31Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13965","volume":81,"issue":"8","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"file":[{"checksum":"a294cd9506b80ed6ef218ef44ed32765","file_id":"13980","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-07T08:32:26Z","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","creator":"dernst","date_updated":"2023-08-07T08:32:26Z","file_size":2568632}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 81","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."}],"pmid":1,"oa_version":"Published Version","author":[{"full_name":"Hollwey, Elizabeth","last_name":"Hollwey","first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"last_name":"Briffa","full_name":"Briffa, Amy","first_name":"Amy"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37441873"],"isi":["001047020200001"]},"title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","citation":{"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.","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.","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","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","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"102087","date_published":"2023-08-01T00:00:00Z","doi":"10.1016/j.gde.2023.102087","date_created":"2023-08-06T22:01:10Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Current Opinion in Genetics and Development","quality_controlled":"1","publisher":"Elsevier","oa":1},{"file":[{"date_created":"2023-08-16T18:15:17Z","file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","file_size":10891454,"file_id":"14075","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","access_level":"closed","relation":"source_file","content_type":"application/zip"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14079","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","file_size":19856686,"date_updated":"2023-08-18T10:47:55Z","creator":"gpuixeus","file_name":"PhDThesis_PuixeuG.pdf","date_created":"2023-08-18T10:47:55Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"status":"public","id":"12933","relation":"research_data"},{"relation":"part_of_dissertation","status":"public","id":"6831"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"08","alternative_title":["ISTA Thesis"],"ddc":["576"],"supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_updated":"2023-12-13T12:15:36Z","file_date_updated":"2023-08-18T10:47:55Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"14058","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"15","has_accepted_license":"1","year":"2023","date_published":"2023-08-15T00:00:00Z","doi":"10.15479/at:ista:14058","date_created":"2023-08-15T10:20:40Z","page":"230","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","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.","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.","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","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","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.","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."},"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala"}],"article_processing_charge":"No","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}]},{"date_created":"2023-08-18T06:52:14Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1093/g3journal/jkad121","publication":"G3: Genes, Genomes, Genetics","day":"01","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","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).","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","article_processing_charge":"Yes","external_id":{"isi":["001002997200001"]},"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (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","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","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.","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).","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."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"ec_funded":1,"issue":"8","volume":13,"related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","file_size":845642,"date_updated":"2023-11-07T09:00:19Z","creator":"dernst","file_name":"2023_G3_Puixeu.pdf","date_created":"2023-11-07T09:00:19Z"}],"publication_status":"published","publication_identifier":{"issn":["2160-1836"]},"intvolume":" 13","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2023-11-07T09:00:19Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"ddc":["570"],"date_updated":"2023-12-13T12:15:37Z","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14077"},{"date_updated":"2023-12-13T12:14:52Z","ddc":["000"],"file_date_updated":"2023-08-22T06:37:48Z","department":[{"_id":"ElKo"}],"_id":"13988","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"status":"public","publication_status":"published","publication_identifier":{"issn":["2169-3536"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"4b80b0ff212edf7e5842fbdd53784432","file_id":"14166","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_IEEEAccess_Neiheiser.pdf","date_created":"2023-08-22T06:37:48Z","creator":"dernst","file_size":1289285,"date_updated":"2023-08-22T06:37:48Z"}],"volume":11,"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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"08","citation":{"chicago":"Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/access.2023.3237897.","ista":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.","mla":"Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access, vol. 11, Institute of Electrical and Electronics Engineers, 2023, pp. 8651–62, doi:10.1109/access.2023.3237897.","apa":"Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., & Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. IEEE Access. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/access.2023.3237897","ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. IEEE Access. 2023;11:8651-8662. doi:10.1109/access.2023.3237897","ieee":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” IEEE Access, vol. 11. Institute of Electrical and Electronics Engineers, pp. 8651–8662, 2023.","short":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"isi":["000927831000001"]},"author":[{"first_name":"Ray","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","last_name":"Neiheiser","orcid":"0000-0001-7227-8309","full_name":"Neiheiser, Ray"},{"first_name":"Gustavo","last_name":"Inacio","full_name":"Inacio, Gustavo"},{"full_name":"Rech, Luciana","last_name":"Rech","first_name":"Luciana"},{"first_name":"Carlos","full_name":"Montez, Carlos","last_name":"Montez"},{"full_name":"Matos, Miguel","last_name":"Matos","first_name":"Miguel"},{"full_name":"Rodrigues, Luis","last_name":"Rodrigues","first_name":"Luis"}],"title":"Practical limitations of Ethereum’s layer-2","year":"2023","has_accepted_license":"1","isi":1,"publication":"IEEE Access","day":"01","page":"8651-8662","date_created":"2023-08-09T12:09:57Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1109/access.2023.3237897","acknowledgement":"This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. 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.","oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers"},{"citation":{"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.","apa":"Puixeu Sala, G. (2023). 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. https://doi.org/10.15479/AT:ISTA:12933","ama":"Puixeu Sala G. 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","ieee":"G. Puixeu Sala, “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.","short":"G. Puixeu Sala, (2023).","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.","ista":"Puixeu Sala G. 2023. 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, 10.15479/AT:ISTA:12933."},"date_updated":"2023-12-13T12:15:36Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2023-05-11T12:50:18Z","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"12933","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","file":[{"content_type":"text/csv","access_level":"open_access","relation":"main_file","checksum":"0ba0bcd0bb8b18d84792136a4370df90","file_id":"12934","success":1,"date_updated":"2023-05-10T09:41:43Z","file_size":8029982,"creator":"gpuixeus","date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S1.csv"},{"success":1,"file_id":"12935","checksum":"a62aa9a6d4904e0fdb699cf752640863","content_type":"text/csv","relation":"main_file","access_level":"open_access","file_name":"Dataset_S2.csv","date_created":"2023-05-10T09:41:43Z","file_size":13667640,"date_updated":"2023-05-10T09:41:43Z","creator":"gpuixeus"},{"content_type":"text/csv","relation":"main_file","access_level":"open_access","success":1,"file_id":"12936","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","file_size":8369141,"date_updated":"2023-05-10T09:41:48Z","creator":"gpuixeus","file_name":"Dataset_S3.csv","date_created":"2023-05-10T09:41:48Z"},{"file_size":19543247,"date_updated":"2023-05-10T09:41:50Z","creator":"gpuixeus","file_name":"Dataset_S4.csv","date_created":"2023-05-10T09:41:50Z","content_type":"text/csv","relation":"main_file","access_level":"open_access","success":1,"checksum":"f6156e5fc44446c907ddd0d7289d4cf8","file_id":"12937"},{"creator":"gpuixeus","file_size":4566,"date_updated":"2023-05-11T12:50:18Z","file_name":"readme.txt","date_created":"2023-05-11T12:50:18Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","success":1,"file_id":"12944","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86"}],"day":"15","date_published":"2023-05-15T00:00:00Z","related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"status":"public","id":"14077","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:12933","date_created":"2023-05-10T10:00:49Z","contributor":[{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"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"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"05"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14245","file_date_updated":"2023-09-05T07:26:17Z","department":[{"_id":"TiBr"}],"date_updated":"2023-12-13T12:19:42Z","ddc":["510"],"scopus_import":"1","intvolume":" 324","month":"07","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","issue":"2","volume":324,"publication_status":"published","publication_identifier":{"issn":["0030-8730"],"eissn":["1945-5844"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a675b53cfb31fa46be1e879b7e77fe8c","file_id":"14267","success":1,"creator":"dernst","date_updated":"2023-09-05T07:26:17Z","file_size":654895,"date_created":"2023-09-05T07:26:17Z","file_name":"2023_PacificJourMaths_Horesh.pdf"}],"article_processing_charge":"Yes","external_id":{"arxiv":["1612.08215"],"isi":["001047690500001"]},"author":[{"full_name":"Horesh, Tal","last_name":"Horesh","id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","first_name":"Tal"},{"last_name":"Nevo","full_name":"Nevo, Amos","first_name":"Amos"}],"title":"Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution","citation":{"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.","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.","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.","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.","short":"T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","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.","page":"265-294","date_created":"2023-08-27T22:01:18Z","doi":"10.2140/pjm.2023.324.265","date_published":"2023-07-26T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Pacific Journal of Mathematics","day":"26"},{"status":"public","keyword":["General Physics and Astronomy"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14246","file_date_updated":"2023-09-05T08:45:49Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-12-13T12:21:09Z","month":"08","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","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."}],"volume":6,"file":[{"success":1,"file_id":"14268","checksum":"6edfc59b0ee7dc406d0968b05236e83d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_CommPhysics_Brauneis.pdf","date_created":"2023-09-05T08:45:49Z","creator":"dernst","file_size":855960,"date_updated":"2023-09-05T08:45:49Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2399-3650"]},"publication_status":"published","article_number":"224","title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"last_name":"Hammer","full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (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","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","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.","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."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","date_published":"2023-08-22T00:00:00Z","doi":"10.1038/s42005-023-01281-2","date_created":"2023-08-28T12:36:49Z","day":"22","publication":"Communications Physics","has_accepted_license":"1","isi":1,"year":"2023"},{"date_created":"2023-08-27T22:01:16Z","doi":"10.1017/fms.2023.65","date_published":"2023-08-03T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Forum of Mathematics, Sigma","day":"03","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","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","external_id":{"isi":["001041926700001"],"arxiv":["2212.06786"]},"article_processing_charge":"Yes","author":[{"full_name":"Mauri, Mirko","last_name":"Mauri","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","first_name":"Mirko"},{"full_name":"Shinder, Evgeny","last_name":"Shinder","first_name":"Evgeny"}],"title":"Homological Bondal-Orlov localization conjecture for rational singularities","citation":{"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","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","ieee":"M. Mauri and E. Shinder, “Homological Bondal-Orlov localization conjecture for rational singularities,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023.","short":"M. Mauri, E. Shinder, Forum of Mathematics, Sigma 11 (2023).","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.","ista":"Mauri M, Shinder E. 2023. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 11, e66.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"article_number":"e66","ec_funded":1,"volume":11,"publication_status":"published","publication_identifier":{"eissn":["2050-5094"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c36241750cc5cb06890aec0ecdfee626","file_id":"14266","success":1,"date_updated":"2023-09-05T06:43:11Z","file_size":280865,"creator":"dernst","date_created":"2023-09-05T06:43:11Z","file_name":"2023_ForumMathematics_Mauri.pdf"}],"scopus_import":"1","intvolume":" 11","month":"08","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 ."}],"oa_version":"Published Version","department":[{"_id":"TaHa"}],"file_date_updated":"2023-09-05T06:43:11Z","date_updated":"2023-12-13T12:18:18Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14239"},{"author":[{"first_name":"Jonas","last_name":"Lampart","full_name":"Lampart, Jonas"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes"},{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"}],"external_id":{"arxiv":["2206.14708"],"isi":["001032992600001"]},"article_processing_charge":"Yes (via OA deal)","title":"On the global minimum of the energy–momentum relation for the polaron","citation":{"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.","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","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","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.","short":"J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023).","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"17","doi":"10.1007/s11040-023-09460-x","date_published":"2023-07-26T00:00:00Z","date_created":"2023-08-22T14:09:47Z","has_accepted_license":"1","isi":1,"year":"2023","day":"26","publication":"Mathematical Physics, Analysis and Geometry","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","department":[{"_id":"RoSe"}],"file_date_updated":"2023-08-23T10:59:15Z","date_updated":"2023-12-13T12:16:19Z","ddc":["510"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Geometry and Topology","Mathematical Physics"],"_id":"14192","issue":"3","volume":26,"publication_identifier":{"issn":["1385-0172"],"eissn":["1572-9656"]},"publication_status":"published","file":[{"file_name":"2023_MathPhysics_Lampart.pdf","date_created":"2023-08-23T10:59:15Z","creator":"dernst","file_size":317026,"date_updated":"2023-08-23T10:59:15Z","success":1,"checksum":"f0941cc66cb3ed06a12ca4b7e356cfd6","file_id":"14225","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 26","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."}],"oa_version":"Published Version"},{"issue":"5","volume":131,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","month":"08","intvolume":" 131","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2308.15247"}],"pmid":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"MiLe"}],"date_updated":"2023-12-13T12:18:54Z","status":"public","article_type":"original","type":"journal_article","_id":"14238","doi":"10.1103/PhysRevLett.131.053201","date_published":"2023-08-04T00:00:00Z","date_created":"2023-08-27T22:01:16Z","day":"04","publication":"Physical Review Letters","isi":1,"year":"2023","publisher":"American Physical Society","quality_controlled":"1","oa":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.","title":"Nonadiabatic laser-induced alignment dynamics of molecules on a surface","author":[{"first_name":"Lorenz","full_name":"Kranabetter, Lorenz","last_name":"Kranabetter"},{"last_name":"Kristensen","full_name":"Kristensen, Henrik H.","first_name":"Henrik H."},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"full_name":"Janssen, Paul","last_name":"Janssen","first_name":"Paul"},{"full_name":"Jensen, Frank","last_name":"Jensen","first_name":"Frank"},{"last_name":"Zillich","full_name":"Zillich, Robert E.","first_name":"Robert E."},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"first_name":"Henrik","full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt"}],"article_processing_charge":"No","external_id":{"isi":["001101784100001"],"pmid":["37595218"],"arxiv":["2308.15247"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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)."},"project":[{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"article_number":"053201"},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 19","publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"publication_status":"published","file":[{"date_created":"2023-09-06T06:41:52Z","file_name":"2023_PloSPathogens_Koch.pdf","date_updated":"2023-09-06T06:41:52Z","file_size":4458336,"creator":"dernst","file_id":"14269","checksum":"47ca3bb54b27f28b05644be0ad064bc6","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"8","volume":19,"_id":"14255","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-12-13T12:22:22Z","ddc":["570"],"file_date_updated":"2023-09-06T06:41:52Z","department":[{"_id":"FlSc"}],"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.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"14","publication":"PLoS Pathogens","doi":"10.1371/journal.ppat.1011562","date_published":"2023-08-14T00:00:00Z","date_created":"2023-09-03T22:01:14Z","article_number":"e1011562","project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"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).","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jana","last_name":"Koch","full_name":"Koch, Jana"},{"first_name":"Qilin","full_name":"Xin, Qilin","last_name":"Xin"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564"},{"last_name":"Schäfer","full_name":"Schäfer, Alicia","first_name":"Alicia"},{"first_name":"Nina","full_name":"Rolfs, Nina","last_name":"Rolfs"},{"first_name":"Holda A.","full_name":"Anagho, Holda A.","last_name":"Anagho"},{"first_name":"Aiste","full_name":"Kudulyte, Aiste","last_name":"Kudulyte"},{"first_name":"Lea","full_name":"Woltereck, Lea","last_name":"Woltereck"},{"last_name":"Kummer","full_name":"Kummer, Susann","first_name":"Susann"},{"first_name":"Joaquin","full_name":"Campos, Joaquin","last_name":"Campos"},{"first_name":"Zina M.","last_name":"Uckeley","full_name":"Uckeley, Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"last_name":"Schur","full_name":"Schur, Florian Km","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km"},{"first_name":"Claudio","full_name":"Acuna, Claudio","last_name":"Acuna"},{"first_name":"Pierre Yves","last_name":"Lozach","full_name":"Lozach, Pierre Yves"}],"article_processing_charge":"Yes","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells"},{"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Nature Plants","page":"1500-1513","doi":"10.1038/s41477-023-01478-x","date_published":"2023-09-01T00:00:00Z","date_created":"2023-09-15T09:56:01Z","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.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Roychoudhry, S","last_name":"Roychoudhry","first_name":"S"},{"first_name":"K","full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas"},{"first_name":"C","full_name":"Wolverton, C","last_name":"Wolverton"},{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","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"},{"full_name":"De Angelis, M","last_name":"De Angelis","first_name":"M"},{"full_name":"Goodman, HL","last_name":"Goodman","first_name":"HL"},{"first_name":"N","last_name":"Capstaff","full_name":"Capstaff, N"},{"first_name":"Lloyd","last_name":"JPB","full_name":"JPB, Lloyd"},{"first_name":"J","full_name":"Mullen, J","last_name":"Mullen"},{"last_name":"Hangarter","full_name":"Hangarter, R","first_name":"R"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37666965"],"isi":["001069238800014"]},"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","file":[{"file_id":"14351","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-09-20T10:51:31Z","file_name":"2023_NaturePlants_Roychoudhry.pdf","date_updated":"2023-09-20T10:51:31Z","file_size":9647103,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":9,"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"}],"oa_version":"Published Version","pmid":1,"month":"09","intvolume":" 9","date_updated":"2023-12-13T12:23:49Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2023-09-20T10:51:31Z","_id":"14339","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"_id":"14363","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-12-13T12:27:30Z","department":[{"_id":"SaSi"}],"file_date_updated":"2023-11-07T08:53:21Z","oa_version":"Published Version","pmid":1,"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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"month":"10","intvolume":" 26","scopus_import":"1","file":[{"file_id":"14497","checksum":"be1a560efdd96d20712311f4fc54aac2","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-11-07T08:53:21Z","file_name":"2023_iScience_Maes.pdf","creator":"dernst","date_updated":"2023-11-07T08:53:21Z","file_size":8197935}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2589-0042"]},"publication_status":"published","volume":26,"issue":"10","article_number":"107780","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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).","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.","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","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"},"title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E"},{"first_name":"Felix","last_name":"Sternberg","full_name":"Sternberg, Felix"},{"first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"first_name":"Elena E.","last_name":"Pohl","full_name":"Pohl, Elena E."},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert"}],"external_id":{"isi":["001080403500001"],"pmid":["37731609"]},"article_processing_charge":"Yes","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.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"20","publication":"iScience","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-10-20T00:00:00Z","doi":"10.1016/j.isci.2023.107780","date_created":"2023-09-24T22:01:11Z"},{"date_published":"2023-08-23T00:00:00Z","doi":"10.1017/fms.2023.70","date_created":"2023-09-17T22:01:09Z","day":"23","publication":"Forum of Mathematics, Sigma","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"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.","title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henheik","orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61","first_name":"Oleksii","last_name":"Kolupaiev","full_name":"Kolupaiev, Oleksii"}],"external_id":{"arxiv":["2301.05181"],"isi":["001051980200001"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","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","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","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."},"project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"article_number":"e74","volume":11,"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14352","checksum":"eb747420e6a88a7796fa934151957676","creator":"dernst","file_size":852652,"date_updated":"2023-09-20T11:09:35Z","file_name":"2023_ForumMathematics_Cipolloni.pdf","date_created":"2023-09-20T11:09:35Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-5094"]},"publication_status":"published","month":"08","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2023-09-20T11:09:35Z","department":[{"_id":"LaEr"},{"_id":"GradSch"}],"ddc":["510"],"date_updated":"2023-12-13T12:24:23Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14343"},{"related_material":{"record":[{"status":"public","id":"6676","relation":"earlier_version"}]},"volume":52,"issue":"4","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"publication_status":"published","month":"07","intvolume":" 52","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"DaAl"}],"date_updated":"2023-12-13T12:28:29Z","status":"public","article_type":"original","type":"journal_article","_id":"14364","date_published":"2023-07-25T00:00:00Z","doi":"10.1137/20M1375851","date_created":"2023-09-24T22:01:11Z","page":"913-944","day":"25","publication":"SIAM Journal on Computing","isi":1,"year":"2023","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":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.","title":"Why extension-based proofs fail","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5","first_name":"Leqi","last_name":"Zhu","full_name":"Zhu, Leqi"}],"external_id":{"arxiv":["1811.01421"],"isi":["001082972300004"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","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.","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."},"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}]},{"date_updated":"2023-12-13T12:25:06Z","department":[{"_id":"HeEd"}],"_id":"14345","article_type":"original","type":"journal_article","status":"public","publication_status":"epub_ahead","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"language":[{"iso":"eng"}],"ec_funded":1,"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"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1007/s00454-023-00566-1","open_access":"1"}],"scopus_import":"1","month":"09","citation":{"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.","short":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023).","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2204.01076"],"isi":["001060727600004"]},"author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Alexey","last_name":"Garber","full_name":"Garber, Alexey"},{"first_name":"Mohadese","full_name":"Ghafari, Mohadese","last_name":"Ghafari"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","last_name":"Heiss"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"title":"On angles in higher order Brillouin tessellations and related tilings in the plane","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"year":"2023","isi":1,"publication":"Discrete and Computational Geometry","day":"07","date_created":"2023-09-17T22:01:10Z","date_published":"2023-09-07T00:00:00Z","doi":"10.1007/s00454-023-00566-1","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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Emmi","last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi"},{"first_name":"Inam","full_name":"Liaqat, Inam","last_name":"Liaqat"},{"first_name":"Emma","last_name":"Jakobsson","full_name":"Jakobsson, Emma"},{"full_name":"Nurmi, Harri","last_name":"Nurmi","first_name":"Harri"},{"last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","citation":{"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.","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.","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).","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"5878","doi":"10.1038/s41467-023-41456-7","date_published":"2023-09-21T00:00:00Z","date_created":"2023-10-01T22:01:13Z","has_accepted_license":"1","isi":1,"year":"2023","day":"21","publication":"Nature Communications","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","file_date_updated":"2023-10-03T07:46:36Z","department":[{"_id":"EdHa"}],"date_updated":"2023-12-13T12:31:05Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14378","volume":14,"ec_funded":1,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"file_id":"14384","checksum":"4fe5423403f2531753bcd9e0fea48e05","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-10-03T07:46:36Z","file_name":"2023_NatureComm_Ucar.pdf","creator":"dernst","date_updated":"2023-10-03T07:46:36Z","file_size":8143264}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 14","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version"}]