[{"month":"01","date_published":"2024-01-19T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2024-01-26T12:00:54Z","day":"19","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ddc":["576"],"publication_identifier":{"issn":["2663 - 337X"]},"_id":"14711","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"article_processing_charge":"No","type":"dissertation","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O"}],"year":"2024","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"10658","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10787","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14732"}]},"title":"Local adaptation, genetic load and extinction in metapopulations","date_created":"2023-12-26T22:49:53Z","alternative_title":["ISTA Thesis"],"citation":{"ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"file":[{"date_updated":"2024-01-03T18:30:13Z","content_type":"application/zip","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_id":"14730","access_level":"closed","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","creator":"oolusany","date_created":"2024-01-03T18:30:13Z","file_size":16986244,"relation":"source_file"},{"file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","access_level":"open_access","creator":"oolusany","date_created":"2024-01-03T18:31:34Z","file_size":6460403,"relation":"main_file","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_id":"14731","content_type":"application/pdf","date_updated":"2024-01-03T18:31:34Z","success":1}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"degree_awarded":"PhD","doi":"10.15479/at:ista:14711","file_date_updated":"2024-01-03T18:31:34Z","acknowledged_ssus":[{"_id":"SSU"}],"page":"183","oa":1},{"publication":"31st International Symposium on Graph Drawing and Network Visualization","intvolume":" 14466","publication_status":"published","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"status":"public","year":"2024","date_created":"2024-01-28T23:01:43Z","title":"Removing popular faces in curve arrangements","alternative_title":["LNCS"],"citation":{"chicago":"De Nooijer, Phoebe, Soeren Terziadis, Alexandra Weinberger, Zuzana Masárová, Tamara Mchedlidze, Maarten Löffler, and Günter Rote. “Removing Popular Faces in Curve Arrangements.” In 31st International Symposium on Graph Drawing and Network Visualization, 14466:18–33. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49275-4_2.","ista":"De Nooijer P, Terziadis S, Weinberger A, Masárová Z, Mchedlidze T, Löffler M, Rote G. 2024. Removing popular faces in curve arrangements. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14466, 18–33.","apa":"De Nooijer, P., Terziadis, S., Weinberger, A., Masárová, Z., Mchedlidze, T., Löffler, M., & Rote, G. (2024). Removing popular faces in curve arrangements. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14466, pp. 18–33). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49275-4_2","ieee":"P. De Nooijer et al., “Removing popular faces in curve arrangements,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14466, pp. 18–33.","ama":"De Nooijer P, Terziadis S, Weinberger A, et al. Removing popular faces in curve arrangements. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14466. Springer Nature; 2024:18-33. doi:10.1007/978-3-031-49275-4_2","mla":"De Nooijer, Phoebe, et al. “Removing Popular Faces in Curve Arrangements.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14466, Springer Nature, 2024, pp. 18–33, doi:10.1007/978-3-031-49275-4_2.","short":"P. De Nooijer, S. Terziadis, A. Weinberger, Z. Masárová, T. Mchedlidze, M. Löffler, G. Rote, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 18–33."},"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2202.12175","open_access":"1"}],"page":"18-33","oa":1,"abstract":[{"text":"A face in a curve arrangement is called popular if it is bounded by the same curve multiple times. Motivated by the automatic generation of curved nonogram puzzles, we investigate possibilities to eliminate the popular faces in an arrangement by inserting a single additional curve. This turns out to be NP-hard; however, it becomes tractable when the number of popular faces is small: We present a probabilistic FPT-approach in the number of popular faces.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-49275-4_2","date_published":"2024-01-06T00:00:00Z","external_id":{"arxiv":["2202.12175"]},"language":[{"iso":"eng"}],"conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2023-09-22","start_date":"2023-09-20","location":"Isola delle Femmine, Palermo, Italy"},"month":"01","day":"06","date_updated":"2024-01-29T09:45:06Z","quality_controlled":"1","acknowledgement":"This work was initiated at the 16th European Research Week on Geometric Graphs in Strobl in 2019. A.W. is supported by the Austrian Science Fund (FWF): W1230. S.T. has been funded by the Vienna Science and Technology Fund (WWTF) [10.47379/ICT19035]. A preliminary version of this work has been presented at the 38th European Workshop on Computational Geometry (EuroCG 2022) in Perugia [9]. A full version of this paper, which includes appendices but is otherwise identical, is available as a technical report [10].","article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031492747"],"eissn":["1611-3349"]},"_id":"14888","publisher":"Springer Nature","author":[{"first_name":"Phoebe","last_name":"De Nooijer","full_name":"De Nooijer, Phoebe"},{"full_name":"Terziadis, Soeren","last_name":"Terziadis","first_name":"Soeren"},{"full_name":"Weinberger, Alexandra","last_name":"Weinberger","first_name":"Alexandra"},{"first_name":"Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová","full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamara","last_name":"Mchedlidze","full_name":"Mchedlidze, Tamara"},{"last_name":"Löffler","full_name":"Löffler, Maarten","first_name":"Maarten"},{"last_name":"Rote","full_name":"Rote, Günter","first_name":"Günter"}],"type":"conference","scopus_import":"1","volume":14466},{"type":"journal_article","scopus_import":"1","author":[{"last_name":"Feitosa Tomé","full_name":"Feitosa Tomé, Douglas","id":"0eed2d40-3d48-11ec-8d38-f789cc2e40b2","first_name":"Douglas"},{"first_name":"Ying","last_name":"Zhang","full_name":"Zhang, Ying"},{"full_name":"Aida, Tomomi","last_name":"Aida","first_name":"Tomomi"},{"first_name":"Olivia","last_name":"Mosto","full_name":"Mosto, Olivia"},{"first_name":"Yifeng","full_name":"Lu, Yifeng","last_name":"Lu"},{"last_name":"Chen","full_name":"Chen, Mandy","first_name":"Mandy"},{"last_name":"Sadeh","full_name":"Sadeh, Sadra","first_name":"Sadra"},{"full_name":"Roy, Dheeraj S.","last_name":"Roy","first_name":"Dheeraj S."},{"full_name":"Clopath, Claudia","last_name":"Clopath","first_name":"Claudia"}],"publisher":"Springer Nature","_id":"14887","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"acknowledgement":"We thank S. Erisken from Inscopix for helping us establish in vivo one-photon calcium imaging for this work. We thank K. Su at Tsinghua University for assistance with this work. This work was funded by the President’s PhD Scholarship from Imperial College London (D.F.T.), the Wellcome Trust (225412/Z/22/Z) (S.S.), the Biotechnology and Biological Sciences Research Council (BB/N013956/1 and BB/N019008/1) (C.C.), the Wellcome Trust (200790/Z/16/Z) (C.C.), the Simons Foundation (564408) (C.C.) and the Engineering and Physical Sciences Research Council (EP/R035806/1) (CC). The School of Life Sciences and the IDG/McGovern Institute for Brain Research supported Y.Z. The Warren Alpert Distinguished Scholar Award and National Institutes of Health 1K99NS125131-01 supported D.S.R.","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","date_updated":"2024-01-29T09:22:00Z","day":"19","isi":1,"month":"01","language":[{"iso":"eng"}],"external_id":{"isi":["001145442300001"]},"date_published":"2024-01-19T00:00:00Z","doi":"10.1038/s41593-023-01551-w","abstract":[{"lang":"eng","text":"Episodic memories are encoded by experience-activated neuronal ensembles that remain necessary and sufficient for recall. However, the temporal evolution of memory engrams after initial encoding is unclear. In this study, we employed computational and experimental approaches to examine how the neural composition and selectivity of engrams change with memory consolidation. Our spiking neural network model yielded testable predictions: memories transition from unselective to selective as neurons drop out of and drop into engrams; inhibitory activity during recall is essential for memory selectivity; and inhibitory synaptic plasticity during memory consolidation is critical for engrams to become selective. Using activity-dependent labeling, longitudinal calcium imaging and a combination of optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted contextual fear conditioning experiments that supported our model’s predictions. Our results reveal that memory engrams are dynamic and that changes in engram composition mediated by inhibitory plasticity are crucial for the emergence of memory selectivity."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"related_material":{"record":[{"id":"14892","status":"public","relation":"research_data"}]},"main_file_link":[{"url":"https://doi.org/10.1038/s41593-023-01551-w","open_access":"1"}],"oa_version":"Published Version","citation":{"ama":"Feitosa Tomé D, Zhang Y, Aida T, et al. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. 2024. doi:10.1038/s41593-023-01551-w","short":"D. Feitosa Tomé, Y. Zhang, T. Aida, O. Mosto, Y. Lu, M. Chen, S. Sadeh, D.S. Roy, C. Clopath, Nature Neuroscience (2024).","mla":"Feitosa Tomé, Douglas, et al. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-023-01551-w.","ista":"Feitosa Tomé D, Zhang Y, Aida T, Mosto O, Lu Y, Chen M, Sadeh S, Roy DS, Clopath C. 2024. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience.","chicago":"Feitosa Tomé, Douglas, Ying Zhang, Tomomi Aida, Olivia Mosto, Yifeng Lu, Mandy Chen, Sadra Sadeh, Dheeraj S. Roy, and Claudia Clopath. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-023-01551-w.","ieee":"D. Feitosa Tomé et al., “Dynamic and selective engrams emerge with memory consolidation,” Nature Neuroscience. Springer Nature, 2024.","apa":"Feitosa Tomé, D., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., … Clopath, C. (2024). Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01551-w"},"date_created":"2024-01-28T23:01:43Z","title":"Dynamic and selective engrams emerge with memory consolidation","year":"2024","department":[{"_id":"TiVo"}],"status":"public","publication_status":"epub_ahead","publication":"Nature Neuroscience"},{"volume":5,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","full_name":"Tang, Han","last_name":"Tang","orcid":"0000-0001-6152-6637","first_name":"Han"},{"full_name":"Lu, KJ","last_name":"Lu","first_name":"KJ"},{"full_name":"Zhang, Y","last_name":"Zhang","first_name":"Y"},{"first_name":"YL","last_name":"Cheng","full_name":"Cheng, YL"},{"first_name":"SL","full_name":"Tu, SL","last_name":"Tu"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"publisher":"Elsevier","_id":"14251","publication_identifier":{"issn":["2590-3462"]},"article_number":"100669","ddc":["580"],"pmid":1,"article_processing_charge":"Yes","acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L.","quality_controlled":"1","date_updated":"2024-01-30T13:00:47Z","day":"08","month":"01","language":[{"iso":"eng"}],"external_id":{"pmid":["37528584"]},"date_published":"2024-01-08T00:00:00Z","doi":"10.1016/j.xplc.2023.100669","file_date_updated":"2024-01-30T12:59:57Z","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2024-01-30T12:59:57Z","file_size":2825565,"creator":"dernst","file_name":"2023_PlantCommunications_Tang.pdf","access_level":"open_access","file_id":"14911","checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a","content_type":"application/pdf","success":1,"date_updated":"2024-01-30T12:59:57Z"}],"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"oa":1,"article_type":"original","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 2024;5(1). doi:10.1016/j.xplc.2023.100669","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” Plant Communications, vol. 5, no. 1, 100669, Elsevier, 2024, doi:10.1016/j.xplc.2023.100669.","chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2023.100669.","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669.","apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., & Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2023.100669","ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” Plant Communications, vol. 5, no. 1. Elsevier, 2024."},"title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution","date_created":"2023-09-01T11:32:02Z","year":"2024","department":[{"_id":"JiFr"}],"status":"public","publication_status":"published","intvolume":" 5","publication":"Plant Communications","issue":"1"},{"issue":"1","intvolume":" 6","publication":"Physical Review Research","department":[{"_id":"ZhAl"}],"status":"public","publication_status":"published","year":"2024","citation":{"ama":"Lorenc D, Alpichshev Z. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013042","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” Physical Review Research, vol. 6, no. 1, 013042, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013042.","short":"D. Lorenc, Z. Alpichshev, Physical Review Research 6 (2024).","ista":"Lorenc D, Alpichshev Z. 2024. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 6(1), 013042.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013042.","ieee":"D. Lorenc and Z. Alpichshev, “Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Lorenc, D., & Alpichshev, Z. (2024). Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013042"},"title":"Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect","date_created":"2024-01-28T23:01:42Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"It is a basic principle that an effect cannot come before the cause. Dispersive relations that follow from this fundamental fact have proven to be an indispensable tool in physics and engineering. They are most powerful in the domain of linear response where they are known as Kramers-Kronig relations. However, when it comes to nonlinear phenomena the implications of causality are much less explored, apart from several notable exceptions. Here in this paper we demonstrate how to apply the dispersive formalism to analyze the ultrafast nonlinear response in the context of the paradigmatic nonlinear Kerr effect. We find that the requirement of causality introduces a noticeable effect even under assumption that Kerr effect is mediated by quasi-instantaneous off-resonant electronic hyperpolarizability. We confirm this by experimentally measuring the time-resolved Kerr dynamics in GaAs by means of a hybrid pump-probe Mach-Zehnder interferometer and demonstrate the presence of an intrinsic lagging between amplitude and phase responses as predicted by dispersive analysis. Our results describe a general property of the time-resolved nonlinear processes thereby highlighting the importance of accounting for dispersive effects in the nonlinear optical processes involving ultrashort pulses."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevResearch.6.013042","file_date_updated":"2024-01-31T11:59:30Z","file":[{"content_type":"application/pdf","success":1,"date_updated":"2024-01-31T11:59:30Z","creator":"dernst","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Lorenc.pdf","relation":"main_file","file_size":2863627,"date_created":"2024-01-31T11:59:30Z","checksum":"42d58f93ae74e7f2c4de058ef75ff8b2","file_id":"14918"}],"language":[{"iso":"eng"}],"date_published":"2024-01-11T00:00:00Z","month":"01","day":"11","date_updated":"2024-01-31T12:01:16Z","acknowledgement":"The work was supported by the Institute of Science and Technology Austria (ISTA). We thank Prof. John M. Dudley, Dr. Ugur Sezer, and Dr. Artem Volosniev for valuable discussions.","article_processing_charge":"Yes","quality_controlled":"1","publication_identifier":{"eissn":["2643-1564"]},"_id":"14886","ddc":["530"],"article_number":"013042","publisher":"American Physical Society","author":[{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan"},{"orcid":"0000-0002-7183-5203","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev"}],"has_accepted_license":"1","volume":6,"type":"journal_article","scopus_import":"1"},{"publisher":"Ubiquity Press","author":[{"first_name":"Keiko","last_name":"Nomura","full_name":"Nomura, Keiko"},{"first_name":"Simon","last_name":"Rella","full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Merritt, Haily","last_name":"Merritt","first_name":"Haily"},{"full_name":"Baltussen, Mathieu","last_name":"Baltussen","first_name":"Mathieu"},{"last_name":"Bird","full_name":"Bird, Darcy","first_name":"Darcy"},{"full_name":"Tjuka, Annika","last_name":"Tjuka","first_name":"Annika"},{"full_name":"Falk, Dan","last_name":"Falk","first_name":"Dan"}],"scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":18,"quality_controlled":"1","article_processing_charge":"Yes","acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","ddc":["550"],"publication_identifier":{"issn":["1875-0281"]},"_id":"14901","day":"11","date_updated":"2024-02-05T10:10:27Z","date_published":"2024-01-11T00:00:00Z","language":[{"iso":"eng"}],"month":"01","article_type":"original","oa":1,"file":[{"success":1,"date_updated":"2024-02-05T10:06:35Z","content_type":"application/pdf","checksum":"b80ebc889033c365d8f8c05a0c655382","file_id":"14939","creator":"dernst","file_name":"2023_IntJourCommons_Nomura.pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-05T10:06:35Z","file_size":1305786}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"file_date_updated":"2024-02-05T10:06:35Z","doi":"10.5334/ijc.1275","date_created":"2024-01-30T11:58:02Z","title":"Tipping points of space debris in low earth orbit","citation":{"ieee":"K. Nomura et al., “Tipping points of space debris in low earth orbit,” International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., & Falk, D. (2024). Tipping points of space debris in low earth orbit. International Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275","chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.","ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024, doi:10.5334/ijc.1275.","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"keyword":["Sociology and Political Science"],"year":"2024","issue":"1","publication":"International Journal of the Commons","intvolume":" 18"},{"department":[{"_id":"JuFi"}],"status":"public","publication_status":"epub_ahead","year":"2024","issue":"2","intvolume":" 34","publication":"Journal of Nonlinear Science","article_type":"original","oa":1,"abstract":[{"text":"We perform a stochastic homogenization analysis for composite materials exhibiting a random microstructure. Under the assumptions of stationarity and ergodicity, we characterize the Gamma-limit of a micromagnetic energy functional defined on magnetizations taking value in the unit sphere and including both symmetric and antisymmetric exchange contributions. This Gamma-limit corresponds to a micromagnetic energy functional with homogeneous coefficients. We provide explicit formulas for the effective magnetic properties of the composite material in terms of homogenization correctors. Additionally, the variational analysis of the two exchange energy terms is performed in the more general setting of functionals defined on manifold-valued maps with Sobolev regularity, in the case in which the target manifold is a bounded, orientable smooth surface with tubular neighborhood of uniform thickness. Eventually, we present an explicit characterization of minimizers of the effective exchange in the case of magnetic multilayers, providing quantitative evidence of Dzyaloshinskii’s predictions on the emergence of helical structures in composite ferromagnetic materials with stochastic microstructure.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00332-023-10005-3","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"citation":{"short":"E. Davoli, L. D’Elia, J. Ingmanns, Journal of Nonlinear Science 34 (2024).","mla":"Davoli, Elisa, et al. “Stochastic Homogenization of Micromagnetic Energies and Emergence of Magnetic Skyrmions.” Journal of Nonlinear Science, vol. 34, no. 2, 30, Springer Nature, 2024, doi:10.1007/s00332-023-10005-3.","ama":"Davoli E, D’Elia L, Ingmanns J. Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. 2024;34(2). doi:10.1007/s00332-023-10005-3","apa":"Davoli, E., D’Elia, L., & Ingmanns, J. (2024). Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-10005-3","ieee":"E. Davoli, L. D’Elia, and J. Ingmanns, “Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions,” Journal of Nonlinear Science, vol. 34, no. 2. Springer Nature, 2024.","ista":"Davoli E, D’Elia L, Ingmanns J. 2024. Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. 34(2), 30.","chicago":"Davoli, Elisa, Lorenza D’Elia, and Jonas Ingmanns. “Stochastic Homogenization of Micromagnetic Energies and Emergence of Magnetic Skyrmions.” Journal of Nonlinear Science. Springer Nature, 2024. https://doi.org/10.1007/s00332-023-10005-3."},"title":"Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions","date_created":"2024-01-28T23:01:42Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05151","open_access":"1"}],"oa_version":"Preprint","day":"23","date_updated":"2024-02-05T08:54:44Z","language":[{"iso":"eng"}],"date_published":"2024-01-23T00:00:00Z","external_id":{"arxiv":["2306.05151"]},"month":"01","publisher":"Springer Nature","author":[{"first_name":"Elisa","last_name":"Davoli","full_name":"Davoli, Elisa"},{"full_name":"D’Elia, Lorenza","last_name":"D’Elia","first_name":"Lorenza"},{"first_name":"Jonas","last_name":"Ingmanns","full_name":"Ingmanns, Jonas","id":"71523d30-15b2-11ec-abd3-f80aa909d6b0"}],"volume":34,"scopus_import":"1","type":"journal_article","acknowledgement":"All authors acknowledge support of the Austrian Science Fund (FWF) through the SFB project F65. The research of E. Davoli and L. D’Elia has additionally been supported by the FWF through grants V662, Y1292, and P35359, as well as from OeAD through the WTZ grant CZ09/2023.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"_id":"14884","article_number":"30"},{"year":"2024","status":"public","department":[{"_id":"MiSi"}],"publication_status":"published","intvolume":" 25","publication":"EMBO reports","issue":"1","abstract":[{"lang":"eng","text":"Centrioles are part of centrosomes and cilia, which are microtubule organising centres (MTOC) with diverse functions. Despite their stability, centrioles can disappear during differentiation, such as in oocytes, but little is known about the regulation of their structural integrity. Our previous research revealed that the pericentriolar material (PCM) that surrounds centrioles and its recruiter, Polo kinase, are downregulated in oogenesis and sufficient for maintaining both centrosome structural integrity and MTOC activity. We now show that the expression of specific components of the centriole cartwheel and wall, including ANA1/CEP295, is essential for maintaining centrosome integrity. We find that Polo kinase requires ANA1 to promote centriole stability in cultured cells and eggs. In addition, ANA1 expression prevents the loss of centrioles observed upon PCM-downregulation. However, the centrioles maintained by overexpressing and tethering ANA1 are inactive, unlike the MTOCs observed upon tethering Polo kinase. These findings demonstrate that several centriole components are needed to maintain centrosome structure. Our study also highlights that centrioles are more dynamic than previously believed, with their structural stability relying on the continuous expression of multiple components."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-05T12:35:03Z","doi":"10.1038/s44319-023-00020-6","file":[{"success":1,"date_updated":"2024-02-05T12:35:03Z","content_type":"application/pdf","checksum":"53c3ef43d9bd6d7bff3ffcf57d763cac","file_id":"14941","creator":"dernst","access_level":"open_access","file_name":"2023_EmboReports_PimentaMarques.pdf","relation":"main_file","file_size":9645056,"date_created":"2024-02-05T12:35:03Z"}],"article_type":"original","oa":1,"page":"102-127","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"apa":"Pimenta-Marques, A., Perestrelo, T., Dos Reis Rodrigues, P., Duarte, P., Ferreira-Silva, A., Lince-Faria, M., & Bettencourt-Dias, M. (2024). Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. Embo Press. https://doi.org/10.1038/s44319-023-00020-6","ieee":"A. Pimenta-Marques et al., “Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM,” EMBO reports, vol. 25, no. 1. Embo Press, pp. 102–127, 2024.","chicago":"Pimenta-Marques, Ana, Tania Perestrelo, Patricia Dos Reis Rodrigues, Paulo Duarte, Ana Ferreira-Silva, Mariana Lince-Faria, and Mónica Bettencourt-Dias. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports. Embo Press, 2024. https://doi.org/10.1038/s44319-023-00020-6.","ista":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, Duarte P, Ferreira-Silva A, Lince-Faria M, Bettencourt-Dias M. 2024. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO reports. 25(1), 102–127.","mla":"Pimenta-Marques, Ana, et al. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports, vol. 25, no. 1, Embo Press, 2024, pp. 102–27, doi:10.1038/s44319-023-00020-6.","short":"A. Pimenta-Marques, T. Perestrelo, P. Dos Reis Rodrigues, P. Duarte, A. Ferreira-Silva, M. Lince-Faria, M. Bettencourt-Dias, EMBO Reports 25 (2024) 102–127.","ama":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, et al. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO reports. 2024;25(1):102-127. doi:10.1038/s44319-023-00020-6"},"date_created":"2024-02-04T23:00:53Z","title":"Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM","date_updated":"2024-02-05T12:37:07Z","day":"10","month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-10T00:00:00Z","volume":25,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Embo Press","author":[{"first_name":"Ana","last_name":"Pimenta-Marques","full_name":"Pimenta-Marques, Ana"},{"first_name":"Tania","last_name":"Perestrelo","full_name":"Perestrelo, Tania"},{"orcid":"0000-0003-1681-508X","first_name":"Patricia","full_name":"Dos Reis Rodrigues, Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues"},{"first_name":"Paulo","last_name":"Duarte","full_name":"Duarte, Paulo"},{"last_name":"Ferreira-Silva","full_name":"Ferreira-Silva, Ana","first_name":"Ana"},{"last_name":"Lince-Faria","full_name":"Lince-Faria, Mariana","first_name":"Mariana"},{"first_name":"Mónica","last_name":"Bettencourt-Dias","full_name":"Bettencourt-Dias, Mónica"}],"publication_identifier":{"eissn":["1469-3178"]},"_id":"14933","ddc":["570"],"acknowledgement":"We thank all members of the Cell Cycle and Regulation Lab for the discussions and for the critical reading of the manuscript. We thank Tomer Avidor-Reiss (University of Toledo, Toledo, OH), Daniel St. Johnston (The Gurdon Institute, Cambridge, UK), David Glover (University of Cambridge, Cambridge, UK), Jingyan Fu (Agricultural University, Beijing, China) Jordan Raff (University of Oxford, Oxford, UK) and Timothy Megraw (Florida State University, Tallahassee, FL) for sharing tools. We acknowledge the technical support of Instituto Gulbenkian de Ciência (IGC)‘s Advanced Imaging Facility, in particular Gabriel Martins, Nuno Pimpão Martins and José Marques. We also thank Tiago Paixão from the IGC’s Quantitative & Digital Science Unit and Marco Louro from the CCR lab for the support provided on statistical analysis. IGC’s Advanced Imaging Facility (AIF-UIC) is supported by the national Portuguese funding ref# PPBI-POCI-01-0145-FEDER -022122. We thank the IGC’s Fly Facility, supported by CONGENTO (LISBOA-01-0145-FEDER-022170). This work was supported by an ERC grant (ERC-2015-CoG-683258) awarded to MBD and a grant from the Portuguese Research Council (FCT) awarded to APM (PTDC/BIA-BID/32225/2017).","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1"},{"date_updated":"2024-02-05T12:43:58Z","year":"2024","status":"public","department":[{"_id":"MaRo"}],"publication_status":"epub_ahead","day":"29","month":"01","publication":"Evolutionary Biology","language":[{"iso":"eng"}],"date_published":"2024-01-29T00:00:00Z","doi":"10.1007/s11692-023-09624-1","abstract":[{"lang":"eng","text":"The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data on antler size in the Irish elk and combined these with comparative data from other deer to test the hypothesis that the gigantic antlers were the outcome of a positive allometry that constrained large-bodied deer to have proportionally even larger antlers. He concluded that the Irish elk had antlers as predicted for its size and interpreted this within his emerging framework of developmental constraints as an explanatory factor in evolution. Here we reanalyze antler allometry based on new morphometric data for 57 taxa of the family Cervidae. We also present a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast to Gould, we find that the antlers of Irish elk were larger than predicted from the allometry within the true deer, Cervini, as analyzed by Gould, but follow the allometry across Cervidae as a whole. After dissecting the discrepancy, we reject the allometric-constraint hypothesis because, contrary to Gould, we find no similarity between static and evolutionary allometries, and because we document extensive non-allometric evolution of antler size across the Cervidae."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","type":"journal_article","oa":1,"author":[{"first_name":"Masahito","full_name":"Tsuboi, Masahito","last_name":"Tsuboi"},{"first_name":"Bjørn Tore","full_name":"Kopperud, Bjørn Tore","last_name":"Kopperud"},{"first_name":"Michael","full_name":"Matschiner, Michael","last_name":"Matschiner"},{"first_name":"Mark","full_name":"Grabowski, Mark","last_name":"Grabowski"},{"last_name":"Syrowatka","id":"205ffb76-7fe7-11eb-aa17-958bd11b99ad","full_name":"Syrowatka, Chrsitine","first_name":"Chrsitine"},{"last_name":"Pélabon","full_name":"Pélabon, Christophe","first_name":"Christophe"},{"first_name":"Thomas F.","last_name":"Hansen","full_name":"Hansen, Thomas F."}],"article_type":"original","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s11692-023-09624-1"}],"_id":"14932","publication_identifier":{"issn":["0071-3260"],"eissn":["1934-2845"]},"oa_version":"Published Version","citation":{"ama":"Tsuboi M, Kopperud BT, Matschiner M, et al. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. 2024. doi:10.1007/s11692-023-09624-1","short":"M. Tsuboi, B.T. Kopperud, M. Matschiner, M. Grabowski, C. Syrowatka, C. Pélabon, T.F. Hansen, Evolutionary Biology (2024).","mla":"Tsuboi, Masahito, et al. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology, Springer Nature, 2024, doi:10.1007/s11692-023-09624-1.","ista":"Tsuboi M, Kopperud BT, Matschiner M, Grabowski M, Syrowatka C, Pélabon C, Hansen TF. 2024. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology.","chicago":"Tsuboi, Masahito, Bjørn Tore Kopperud, Michael Matschiner, Mark Grabowski, Chrsitine Syrowatka, Christophe Pélabon, and Thomas F. Hansen. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology. Springer Nature, 2024. https://doi.org/10.1007/s11692-023-09624-1.","apa":"Tsuboi, M., Kopperud, B. T., Matschiner, M., Grabowski, M., Syrowatka, C., Pélabon, C., & Hansen, T. F. (2024). Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. Springer Nature. https://doi.org/10.1007/s11692-023-09624-1","ieee":"M. Tsuboi et al., “Antler allometry, the Irish elk and Gould revisited,” Evolutionary Biology. Springer Nature, 2024."},"acknowledgement":"Open access funding provided by University of Oslo (incl Oslo University Hospital).\r\nWe thank Adrian Lister, Louis Tomsett, Roberto Portela Miguez and Roula Pappa (NHMUK), Brian O'Toole and Eileen Westwig (AMNH), Daniela Kalthoff (NHRM), Alexander Bibl and Zachos Frank (NHMW), Darrin Lunde and John Ososky (NMNH), Matthew Parkes and Nigel Monaghan (NMI), Elizabetta Cioppi and Luca Bellucci (IGF), and Yoshihiro Tanaka and Hiroyuki Taruno (OMNH), who helped us in obtaining the museum data, and a special thanks to Jørgen Sikkeland (NTNU NHM) for assistance in obtaining the ontogenetic data for the red deer. We thank Olja Toljagic and Kjetil L. Voje for discussions, Ayumu Tsuboi for assistance with data collection, and Jean-Michel Gaillard and the anonymous reviewers for comments on the manuscript. We thank the Centre of Advanced Study (CAS) at the Norwegian Academy of Sciences and Letters for hosting us during the academic year of 2019/2020 when much of the analysis and writing were done. MT was funded by JSPS Research Fellowship for Young Scientists (201603238).","article_processing_charge":"Yes (via OA deal)","title":"Antler allometry, the Irish elk and Gould revisited","date_created":"2024-02-04T23:00:53Z","quality_controlled":"1"},{"author":[{"orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"publisher":"Elsevier","type":"journal_article","scopus_import":"1","volume":286,"quality_controlled":"1","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","article_processing_charge":"Yes (in subscription journal)","article_number":"110320","_id":"14931","publication_identifier":{"eissn":["1096--0783"],"issn":["0022-1236"]},"day":"24","date_updated":"2024-02-05T12:53:21Z","external_id":{"arxiv":["2301.04894"]},"date_published":"2024-01-24T00:00:00Z","language":[{"iso":"eng"}],"month":"01","article_type":"original","oa":1,"project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427"}],"doi":"10.1016/j.jfa.2024.110320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","date_created":"2024-02-04T23:00:53Z","citation":{"apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320"},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.jfa.2024.110320","open_access":"1"}],"ec_funded":1,"publication_status":"epub_ahead","department":[{"_id":"RoSe"}],"status":"public","year":"2024","issue":"7","publication":"Journal of Functional Analysis","intvolume":" 286"},{"oa_version":"Published Version","publication_identifier":{"issn":["0926-2601"],"eissn":["1572-929X"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s11118-023-10118-0"}],"_id":"14934","quality_controlled":"1","title":"A discovery tour in random Riemannian geometry","date_created":"2024-02-04T23:00:54Z","acknowledgement":"The authors would like to thank Matthias Erbar and Ronan Herry for valuable discussions on this project. They are also grateful to Nathanaël Berestycki, and Fabrice Baudoin for respectively pointing out the references [7], and [6, 24], and to Julien Fageot and Thomas Letendre for pointing out a mistake in a previous version of the proof of Proposition 3.10. The authors feel very much indebted to an anonymous reviewer for his/her careful reading and the many valuable suggestions that have significantly contributed to the improvement of the paper. L.D.S. gratefully acknowledges financial support by the Deutsche Forschungsgemeinschaft through CRC 1060 as well as through SPP 2265, and by the Austrian Science Fund (FWF) grant F65 at Institute of Science and Technology Austria. This research was funded in whole or in part by the Austrian Science Fund (FWF) ESPRIT 208. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. E.K. and K.-T.S. gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the Hausdorff Center for Mathematics and through CRC 1060 as well as through SPP 2265.\r\nOpen Access funding enabled and organized by Projekt DEAL.","citation":{"ieee":"L. Dello Schiavo, E. Kopfer, and K. T. Sturm, “A discovery tour in random Riemannian geometry,” Potential Analysis. Springer Nature, 2024.","apa":"Dello Schiavo, L., Kopfer, E., & Sturm, K. T. (2024). A discovery tour in random Riemannian geometry. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-023-10118-0","ista":"Dello Schiavo L, Kopfer E, Sturm KT. 2024. A discovery tour in random Riemannian geometry. Potential Analysis.","chicago":"Dello Schiavo, Lorenzo, Eva Kopfer, and Karl Theodor Sturm. “A Discovery Tour in Random Riemannian Geometry.” Potential Analysis. Springer Nature, 2024. https://doi.org/10.1007/s11118-023-10118-0.","short":"L. Dello Schiavo, E. Kopfer, K.T. Sturm, Potential Analysis (2024).","mla":"Dello Schiavo, Lorenzo, et al. “A Discovery Tour in Random Riemannian Geometry.” Potential Analysis, Springer Nature, 2024, doi:10.1007/s11118-023-10118-0.","ama":"Dello Schiavo L, Kopfer E, Sturm KT. A discovery tour in random Riemannian geometry. Potential Analysis. 2024. doi:10.1007/s11118-023-10118-0"},"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","type":"journal_article","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"abstract":[{"lang":"eng","text":"We study random perturbations of a Riemannian manifold (M, g) by means of so-called\r\nFractional Gaussian Fields, which are defined intrinsically by the given manifold. The fields\r\nh• : ω \u0002→ hω will act on the manifold via the conformal transformation g \u0002→ gω := e2hω g.\r\nOur focus will be on the regular case with Hurst parameter H > 0, the critical case H = 0\r\nbeing the celebrated Liouville geometry in two dimensions. We want to understand how basic\r\ngeometric and functional-analytic quantities like diameter, volume, heat kernel, Brownian\r\nmotion, spectral bound, or spectral gap change under the influence of the noise. And if so, is\r\nit possible to quantify these dependencies in terms of key parameters of the noise? Another\r\ngoal is to define and analyze in detail the Fractional Gaussian Fields on a general Riemannian\r\nmanifold, a fascinating object of independent interest."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s11118-023-10118-0","publisher":"Springer Nature","article_type":"original","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","first_name":"Lorenzo"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor","last_name":"Sturm"}],"oa":1,"publication":"Potential Analysis","month":"01","date_published":"2024-01-26T00:00:00Z","language":[{"iso":"eng"}],"year":"2024","date_updated":"2024-02-05T13:04:23Z","day":"26","publication_status":"epub_ahead","department":[{"_id":"JaMa"}],"status":"public"},{"doi":"10.1007/s00029-023-00908-0","abstract":[{"text":"Let $\\ell$ be a prime number. We classify the subgroups $G$ of $\\operatorname{Sp}_4(\\mathbb{F}_\\ell)$ and $\\operatorname{GSp}_4(\\mathbb{F}_\\ell)$ that act irreducibly on $\\mathbb{F}_\\ell^4$, but such that every element of $G$ fixes an $\\mathbb{F}_\\ell$-vector subspace of dimension 1. We use this classification to prove that the local-global principle for isogenies of degree $\\ell$ between abelian surfaces over number fields holds in many cases -- in particular, whenever the abelian surface has non-trivial endomorphisms and $\\ell$ is large enough with respect to the field of definition. Finally, we prove that there exist arbitrarily large primes $\\ell$ for which some abelian surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree $\\ell$.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2206.15240","open_access":"1"}],"date_created":"2023-01-16T11:45:53Z","title":"On the local-global principle for isogenies of abelian surfaces","citation":{"short":"D. Lombardo, M. Verzobio, Selecta Mathematica 30 (2024).","mla":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” Selecta Mathematica, vol. 30, no. 2, 18, Springer Nature, 2024, doi:10.1007/s00029-023-00908-0.","ama":"Lombardo D, Verzobio M. On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. 2024;30(2). doi:10.1007/s00029-023-00908-0","apa":"Lombardo, D., & Verzobio, M. (2024). On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-023-00908-0","ieee":"D. Lombardo and M. Verzobio, “On the local-global principle for isogenies of abelian surfaces,” Selecta Mathematica, vol. 30, no. 2. Springer Nature, 2024.","chicago":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” Selecta Mathematica. Springer Nature, 2024. https://doi.org/10.1007/s00029-023-00908-0.","ista":"Lombardo D, Verzobio M. 2024. On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. 30(2), 18."},"year":"2024","publication_status":"epub_ahead","status":"public","department":[{"_id":"TiBr"}],"publication":"Selecta Mathematica","intvolume":" 30","issue":"2","scopus_import":"1","type":"journal_article","volume":30,"author":[{"last_name":"Lombardo","full_name":"Lombardo, Davide","first_name":"Davide"},{"last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo","first_name":"Matteo","orcid":"0000-0002-0854-0306"}],"publisher":"Springer Nature","article_number":"18","_id":"12312","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"It is a pleasure to thank Samuele Anni for his interest in this project and for several discussions on the topic of this paper, which led in particular to Remark 6.30 and to a better understanding of the difficulties with [6]. We also thank John Cullinan for correspondence about [6] and Barinder Banwait for his many insightful comments on the first version of this paper. Finally, we thank the referee for their thorough reading of the manuscript.\r\nOpen access funding provided by Università di Pisa within the CRUI-CARE Agreement. The authors have been partially supported by MIUR (Italy) through PRIN 2017 “Geometric, algebraic and analytic methods in arithmetic\" and PRIN 2022 “Semiabelian varieties, Galois representations and related Diophantine problems\", and by the University of Pisa through PRA 2018-19 and 2022 “Spazi di moduli, rappresentazioni e strutture combinatorie\". The first author is a member of the INdAM group GNSAGA.","date_updated":"2024-02-05T12:25:00Z","day":"26","month":"01","external_id":{"arxiv":["2206.15240"]},"date_published":"2024-01-26T00:00:00Z","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The near-surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density-driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on-glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non-linear response of glaciers to an uncertain future.","lang":"eng"}],"doi":"10.1029/2023JD040214","file_date_updated":"2024-02-06T08:38:27Z","file":[{"content_type":"application/pdf","success":1,"date_updated":"2024-02-06T08:38:27Z","creator":"dernst","file_name":"2024_JGRAtmospheres_Shaw.pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-06T08:38:27Z","file_size":7481087,"checksum":"cad5b93caadb40c14e5faedc34f7bba7","file_id":"14943"}],"oa":1,"article_type":"original","related_material":{"record":[{"status":"public","id":"14919","relation":"research_data"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:10.1029/2023JD040214.","short":"T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 129 (2024).","ama":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 2024;129(2). doi:10.1029/2023JD040214","ieee":"T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls on near-surface glacier cooling under warm atmospheric conditions,” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2. Wiley, 2024.","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E. S., & Pellicciotti, F. (2024). Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040214","ista":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 129(2), e2023JD040214.","chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres. Wiley, 2024. https://doi.org/10.1029/2023JD040214."},"date_created":"2024-01-28T23:01:42Z","title":"Local controls on near-surface glacier cooling under warm atmospheric conditions","year":"2024","status":"public","department":[{"_id":"FrPe"}],"publication_status":"published","intvolume":" 129","publication":"Journal of Geophysical Research: Atmospheres","issue":"2","volume":129,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Wiley","author":[{"orcid":"0000-0001-7640-6152","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","full_name":"Shaw, Thomas","last_name":"Shaw"},{"first_name":"Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal","last_name":"Buri"},{"full_name":"Mccarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"Mccarthy","first_name":"Michael"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","orcid":"0000-0002-5554-8087"}],"publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"_id":"14885","ddc":["550"],"article_number":"e2023JD040214","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101026058. The authors acknowledge the invaluable field assistance of Marta Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander Groos. The authors would also like to thank Luca Carturan for advice regarding AWS setup and maintenance and Simone Fatichi for provision and support in the use of the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","date_updated":"2024-02-06T08:44:02Z","day":"28","month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-28T00:00:00Z"},{"year":"2024","keyword":["Public Health","Environmental and Occupational Health","General Environmental Science","Renewable Energy","Sustainability and the Environment"],"department":[{"_id":"FrPe"}],"status":"public","publication_status":"accepted","publication":"Environmental Research Letters","doi":"10.1088/1748-9326/ad25a0","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"High elevation headwater catchments are complex hydrological systems that seasonally buffer water and release it in the form of snow and ice melt, modulating downstream runoff regimes and water availability. In High Mountain Asia (HMA), where a wide range of climates from semi-arid to monsoonal exist, the importance of the cryospheric contributions to the water budget varies with the amount and seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation are to date largely unquantified components of the water budget in such catchments, although they can be comparable in magnitude to glacier melt contributions to streamflow. 
Here, we simulate the hydrology of three high elevation headwater catchments in distinct climates in HMA over 10 years using an ecohydrological model geared towards high-mountain areas including snow and glaciers, forced with reanalysis data. 
Our results show that evapotranspiration and sublimation together are most important at the semi-arid site, Kyzylsu, on the northernmost slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28% of the water throughput, which we define as the total water added to, or removed from the water balance within a year. In comparison, evaporative losses are 19% at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes 15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of 76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found to only partially compensate for the annual supply deficit."}],"article_type":"original","oa":1,"main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/ad25a0","open_access":"1"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"apa":"Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti, F. (n.d.). Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/ad25a0","ieee":"S. Fugger et al., “Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia,” Environmental Research Letters. IOP Publishing.","ista":"Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi S, Kneib M, Molnar P, Pellicciotti F. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters.","chicago":"Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri, Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters. IOP Publishing, n.d. https://doi.org/10.1088/1748-9326/ad25a0.","short":"S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe, S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters (n.d.).","mla":"Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters, IOP Publishing, doi:10.1088/1748-9326/ad25a0.","ama":"Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. doi:10.1088/1748-9326/ad25a0"},"title":"Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia","date_created":"2024-02-05T09:01:11Z","date_updated":"2024-02-06T08:35:39Z","day":"02","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-02T00:00:00Z","has_accepted_license":"1","type":"journal_article","author":[{"full_name":"Fugger, Stefan","id":"86698d64-c4c6-11ee-af02-cdf1e6a7d31f","last_name":"Fugger","first_name":"Stefan"},{"last_name":"Shaw","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas","orcid":"0000-0001-7640-6152"},{"first_name":"Achille","last_name":"Jouberton","full_name":"Jouberton, Achille"},{"full_name":"Miles, Evan","last_name":"Miles","first_name":"Evan"},{"last_name":"Buri","id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal","first_name":"Pascal"},{"full_name":"McCarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"McCarthy","first_name":"Michael"},{"id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise","last_name":"Fyffe","first_name":"Catriona Louise"},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone"},{"first_name":"Marin","full_name":"Kneib, Marin","last_name":"Kneib"},{"last_name":"Molnar","full_name":"Molnar, Peter","first_name":"Peter"},{"orcid":"0000-0002-5554-8087","first_name":"Francesca","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"}],"publisher":"IOP Publishing","_id":"14938","publication_identifier":{"issn":["1748-9326"]},"ddc":["550"],"article_processing_charge":"Yes","quality_controlled":"1"},{"publication":"1st Conference on Parsimony and Learning","month":"01","conference":{"end_date":"2024-01-03","start_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning","location":"Hong Kong, China"},"language":[{"iso":"eng"}],"date_published":"2024-01-03T00:00:00Z","external_id":{"arxiv":["2304.01430"]},"year":"2024","date_updated":"2024-02-12T08:56:23Z","status":"public","department":[{"_id":"FrLo"}],"publication_status":"published","day":"03","_id":"14213","ddc":["000"],"oa_version":"Published Version","citation":{"short":"D. Lao, Z. Hu, F. Locatello, Y. Yang, S. Soatto, in:, 1st Conference on Parsimony and Learning, 2024.","mla":"Lao, Dong, et al. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” 1st Conference on Parsimony and Learning, 2024.","ama":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. Divided attention: Unsupervised multi-object discovery with contextually separated slots. In: 1st Conference on Parsimony and Learning. ; 2024.","ieee":"D. Lao, Z. Hu, F. Locatello, Y. Yang, and S. Soatto, “Divided attention: Unsupervised multi-object discovery with contextually separated slots,” in 1st Conference on Parsimony and Learning, Hong Kong, China, 2024.","apa":"Lao, D., Hu, Z., Locatello, F., Yang, Y., & Soatto, S. (2024). Divided attention: Unsupervised multi-object discovery with contextually separated slots. In 1st Conference on Parsimony and Learning. Hong Kong, China.","ista":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. 2024. Divided attention: Unsupervised multi-object discovery with contextually separated slots. 1st Conference on Parsimony and Learning. CPAL: Conference on Parsimony and Learning.","chicago":"Lao, Dong, Zhengyang Hu, Francesco Locatello, Yanchao Yang, and Stefano Soatto. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” In 1st Conference on Parsimony and Learning, 2024."},"article_processing_charge":"No","quality_controlled":"1","date_created":"2023-08-22T14:19:59Z","title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","file_date_updated":"2024-02-12T08:40:36Z","type":"conference","file":[{"date_updated":"2024-02-12T08:40:36Z","success":1,"content_type":"application/pdf","file_id":"14978","checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","date_created":"2024-02-12T08:40:36Z","file_size":8038511,"relation":"main_file","access_level":"open_access","file_name":"2024_CPAL_Lao.pdf","creator":"dernst"}],"author":[{"last_name":"Lao","full_name":"Lao, Dong","first_name":"Dong"},{"first_name":"Zhengyang","last_name":"Hu","full_name":"Hu, Zhengyang"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"last_name":"Yang","full_name":"Yang, Yanchao","first_name":"Yanchao"},{"first_name":"Stefano","last_name":"Soatto","full_name":"Soatto, Stefano"}],"oa":1},{"date_updated":"2024-02-12T11:49:06Z","day":"05","month":"02","language":[{"iso":"eng"}],"external_id":{"arxiv":["2306.12804"]},"date_published":"2024-02-05T00:00:00Z","has_accepted_license":"1","volume":6,"type":"journal_article","author":[{"orcid":"0000-0003-0582-2946","first_name":"Sofya","full_name":"Agafonova, Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","last_name":"Agafonova"},{"full_name":"Mishra, Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","last_name":"Mishra","first_name":"Umang"},{"orcid":"0000-0002-4947-8924","first_name":"Fritz R","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico"},{"orcid":"0000-0002-2031-204X","first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"}],"publisher":"American Physical Society","_id":"14980","publication_identifier":{"eissn":["2643-1564"]},"ddc":["530"],"article_number":"013141","acknowledgement":"We thank Pere Rosselló for his contributions to the initial modeling of the presented sensing technique. This work was supported by Institute of Science and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","article_processing_charge":"Yes","quality_controlled":"1","year":"2024","department":[{"_id":"OnHo"}],"status":"public","publication_status":"published","intvolume":" 6","publication":"Physical Review Research","issue":"1","doi":"10.1103/physrevresearch.6.013141","file_date_updated":"2024-02-12T11:46:50Z","abstract":[{"lang":"eng","text":"Precision sensing and manipulation of milligram-scale mechanical oscillators has attracted growing interest in the fields of table-top explorations of gravity and tests of quantum mechanics at macroscopic scales. Torsional oscillators present an opportunity in this regard due to their remarked isolation from environmental noise. For torsional motion, an effective employment of optical cavities to enhance optomechanical interactions—as already established for linear oscillators—so far faced certain challenges. Here, we propose a concept for sensing and manipulating torsional motion, where exclusively the torsional rotations of a pendulum are mapped onto the path length of a single two-mirror optical cavity. The concept inherently alleviates many limitations of previous approaches. A proof-of-principle experiment is conducted with a rigidly controlled pendulum to explore the sensing aspects of the concept and to identify practical limitations in a potential state-of-the art setup. Based on this study, we anticipate development of precision torque sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz, while the motion of the pendulums are dominated by quantum radiation pressure noise at sub-microwatts of incoming laser power. These developments will provide horizons for experiments at the interface of quantum mechanics and gravity."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"date_updated":"2024-02-12T11:46:50Z","content_type":"application/pdf","checksum":"3a39ebffb24c1cc1dd0b547a726dc52d","file_id":"14981","creator":"dernst","access_level":"open_access","file_name":"2024_PhysicalRevResearch_Agafonova.pdf","relation":"main_file","file_size":1437167,"date_created":"2024-02-12T11:46:50Z"}],"project":[{"grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"oa":1,"article_type":"original","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013141","short":"S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research 6 (2024).","mla":"Agafonova, Sofya, et al. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research, vol. 6, no. 1, 013141, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013141.","chicago":"Agafonova, Sofya, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013141.","ista":"Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 6(1), 013141.","ieee":"S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity for sensing and controlling torsional motion,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Agafonova, S., Mishra, U., Diorico, F. R., & Hosten, O. (2024). Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013141"},"date_created":"2024-02-12T11:42:18Z","title":"Zigzag optical cavity for sensing and controlling torsional motion"},{"file_date_updated":"2024-01-23T12:18:07Z","doi":"10.1002/piuz.202301690","abstract":[{"text":"Die Quantenrotation ist ein spannendes Phänomen, das in vielen verschiedenen Systemen auftritt, von Molekülen und Atomen bis hin zu subatomaren Teilchen wie Neutronen und Protonen. Durch den Einsatz von starken Laserpulsen ist es möglich, die mathematisch anspruchsvolle Topologie der Rotation von Molekülen aufzudecken und topologisch geschützte Zustände zu erzeugen, die unerwartetes Verhalten zeigen. Diese Entdeckungen könnten Auswirkungen auf die Molekülphysik und physikalische Chemie haben und die Entwicklung neuer Technologien ermöglichen. Die Verbindung von Quantenrotation und Topologie stellt ein aufregendes, interdisziplinäres Forschungsfeld dar und bietet neue Wege zur Kontrolle und Nutzung von quantenmechanischen Phänomenen.","lang":"ger"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"3051dadcf9bc57da97e36b647c596ab1","file_id":"14878","access_level":"open_access","file_name":"2024_PhysikZeit_Karle.pdf","creator":"dernst","date_created":"2024-01-23T12:18:07Z","file_size":1155244,"relation":"main_file","date_updated":"2024-01-23T12:18:07Z","success":1,"content_type":"application/pdf"}],"article_type":"original","oa":1,"page":"28-33","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"V. Karle and M. Lemeshko, “Die faszinierende Topologie rotierender Quanten,” Physik in unserer Zeit, vol. 55, no. 1. Wiley, pp. 28–33, 2024.","apa":"Karle, V., & Lemeshko, M. (2024). Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. Wiley. https://doi.org/10.1002/piuz.202301690","ista":"Karle V, Lemeshko M. 2024. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 55(1), 28–33.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit. Wiley, 2024. https://doi.org/10.1002/piuz.202301690.","short":"V. Karle, M. Lemeshko, Physik in unserer Zeit 55 (2024) 28–33.","mla":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit, vol. 55, no. 1, Wiley, 2024, pp. 28–33, doi:10.1002/piuz.202301690.","ama":"Karle V, Lemeshko M. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 2024;55(1):28-33. doi:10.1002/piuz.202301690"},"date_created":"2024-01-22T08:19:36Z","title":"Die faszinierende Topologie rotierender Quanten","year":"2024","keyword":["General Earth and Planetary Sciences","General Environmental Science"],"department":[{"_id":"MiLe"}],"status":"public","publication_status":"published","intvolume":" 55","publication":"Physik in unserer Zeit","issue":"1","volume":55,"has_accepted_license":"1","type":"journal_article","author":[{"orcid":"0000-0002-6963-0129","first_name":"Volker","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"publisher":"Wiley","_id":"14851","publication_identifier":{"eissn":["1521-3943"],"issn":["0031-9252"]},"ddc":["530"],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","date_updated":"2024-02-15T14:29:04Z","day":"01","month":"01","language":[{"iso":"ger"}],"date_published":"2024-01-01T00:00:00Z"},{"day":"05","date_updated":"2024-02-19T10:22:44Z","date_published":"2024-02-05T00:00:00Z","external_id":{"arxiv":["1810.12491"]},"language":[{"iso":"eng"}],"month":"02","publisher":"Oxford University Press","author":[{"last_name":"Shen","full_name":"Shen, Shiyu","id":"544cccd3-9005-11ec-87bc-94aef1c5b814","first_name":"Shiyu"}],"type":"journal_article","quality_controlled":"1","acknowledgement":"This work was supported by the NSF [DMS-1502125to S.S.]; and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement [101034413 to S.S.].\r\nI would like to thank my advisor Tom Nevins for many helpful discussions on this subject and for his comments on this paper. I would like to thank Christopher Dodd, Michael Groechenig, and Tamas Hausel for helpful conversations. I would like to thank Tsao-Hsien Chen for useful comments on an earlier version of this paper.","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"_id":"14986","publication_status":"epub_ahead","status":"public","department":[{"_id":"TaHa"}],"keyword":["General Mathematics"],"year":"2024","publication":"International Mathematics Research Notices","article_type":"original","oa":1,"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"abstract":[{"text":"We prove a version of the tamely ramified geometric Langlands correspondence in positive characteristic for GLn(k). Let k be an algebraically closed field of characteristic p>n. Let X be a smooth projective curve over k with marked points, and fix a parabolic subgroup of GLn(k) at each marked point. We denote by Bunn,P the moduli stack of (quasi-)parabolic vector bundles on X, and by Locn,P the moduli stack of parabolic flat connections such that the residue is nilpotent with respect to the parabolic reduction at each marked point. We construct an equivalence between the bounded derived category Db(Qcoh(Loc0n,P)) of quasi-coherent sheaves on an open substack Loc0n,P⊂Locn,P, and the bounded derived category Db(D0Bunn,P-mod) of D0Bunn,P-modules, where D0Bunn,P is a localization of DBunn,P the sheaf of crystalline differential operators on Bunn,P. Thus we extend the work of Bezrukavnikov-Braverman to the tamely ramified case. We also prove a correspondence between flat connections on X with regular singularities and meromorphic Higgs bundles on the Frobenius twist X(1) of X with first order poles .","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/imrn/rnae005","date_created":"2024-02-14T12:16:17Z","title":"Tamely ramified geometric Langlands correspondence in positive characteristic","citation":{"ama":"Shen S. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. 2024. doi:10.1093/imrn/rnae005","short":"S. Shen, International Mathematics Research Notices (2024).","mla":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices, Oxford University Press, 2024, doi:10.1093/imrn/rnae005.","ista":"Shen S. 2024. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices.","chicago":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices. Oxford University Press, 2024. https://doi.org/10.1093/imrn/rnae005.","ieee":"S. Shen, “Tamely ramified geometric Langlands correspondence in positive characteristic,” International Mathematics Research Notices. Oxford University Press, 2024.","apa":"Shen, S. (2024). Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnae005"},"oa_version":"Published Version","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1093/imrn/rnae005","open_access":"1"}]},{"article_processing_charge":"No","acknowledgement":"We would like to extend our thanks to members of the Sweeney, Tosches, Shein-Idelson,\r\nYamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion and support.\r\nWe additionally thank the Beckman Institute Clover Center and Viviana Gradinaru (Caltech),\r\nKimberly Ritola (UNC NeuroTools), Flavia Gama Gomez Leite (ISTA Viral Core), and Hüseyin\r\nCihan Önal (Shigemoto Group, ISTA) for their consultation and assistance regarding AAVs, as\r\nwell as Andras Simon and Alberto Joven for feedback and discussions on AAVs in Pleurodeles.\r\nTo do these experiments, we have also benefited from the tremendous support of our animal care and imaging facilities at our respective institutions, as well as the amphibian stock centers\r\n(National Xenopus Resource Center, European Xenopus Resource Center, Xenopus Express)\r\nand our funding sources: U.S. National Science Foundation (NSF) Grant Number IOS 2110086\r\n(D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); United States-Israel Binational Science Foundation\r\n(BSF) Grant Number 2020702 (M.S.-I.); NSF Award Number 1645105 (G.J.G., M.E.H.); FTI\r\nStrategy Lower Austria Dissertation Grant Number FTI21-D-046 (D.V.); Horizon Europe ERC\r\nStarting Grant Number 101041551 (L.B.S.); NIH grant number R35GM146973 (M.A.T.); Rita Allen\r\nFoundation award number GA_032522_FE (M.A.T.); European Molecular Biology Organization\r\nLong-Term Fellowship ALTF 874-2021 (A.D.); National Science Foundation Graduate Research\r\nFellowship DGE 2036197 (E.C.J.B.); NIH grant number P40OD010997 (M.E.H).","citation":{"chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.15.580289.","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv, 10.1101/2024.02.15.580289.","ieee":"E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” bioRxiv. .","apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (n.d.). Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. https://doi.org/10.1101/2024.02.15.580289","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. doi:10.1101/2024.02.15.580289","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, doi:10.1101/2024.02.15.580289.","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, BioRxiv (n.d.)."},"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","date_created":"2024-02-20T09:20:32Z","main_file_link":[{"url":"https://doi.org/10.1101/2024.02.15.580289","open_access":"1"}],"_id":"15016","oa_version":"Preprint","oa":1,"author":[{"full_name":"Jaeger, Eliza C.B.","last_name":"Jaeger","first_name":"Eliza C.B."},{"full_name":"Vijatovic, David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David"},{"first_name":"Astrid","full_name":"Deryckere, Astrid","last_name":"Deryckere"},{"first_name":"Nikol","last_name":"Zorin","full_name":"Zorin, Nikol"},{"first_name":"Akemi L.","full_name":"Nguyen, Akemi L.","last_name":"Nguyen"},{"first_name":"Georgiy","last_name":"Ivanian","full_name":"Ivanian, Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05"},{"first_name":"Jamie","last_name":"Woych","full_name":"Woych, Jamie"},{"first_name":"Rebecca C","last_name":"Arnold","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f","full_name":"Arnold, Rebecca C"},{"first_name":"Alonso","last_name":"Ortega Gurrola","full_name":"Ortega Gurrola, Alonso"},{"last_name":"Shvartsman","full_name":"Shvartsman, Arik","first_name":"Arik"},{"first_name":"Francesca","id":"a9492887-8972-11ed-ae7b-bfae10998254","full_name":"Barbieri, Francesca","last_name":"Barbieri"},{"last_name":"Toma","full_name":"Toma, Florina-Alexandra","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","first_name":"Florina-Alexandra"},{"last_name":"Gorbsky","full_name":"Gorbsky, Gary J.","first_name":"Gary J."},{"first_name":"Marko E.","full_name":"Horb, Marko E.","last_name":"Horb"},{"full_name":"Cline, Hollis T.","last_name":"Cline","first_name":"Hollis T."},{"first_name":"Timothy F.","last_name":"Shay","full_name":"Shay, Timothy F."},{"first_name":"Darcy B.","last_name":"Kelley","full_name":"Kelley, Darcy B."},{"full_name":"Yamaguchi, Ayako","last_name":"Yamaguchi","first_name":"Ayako"},{"first_name":"Mark","full_name":"Shein-Idelson, Mark","last_name":"Shein-Idelson"},{"first_name":"Maria Antonietta","full_name":"Tosches, Maria Antonietta","last_name":"Tosches"},{"last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"}],"doi":"10.1101/2024.02.15.580289","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at the transition between aquatic and terrestrial lifestyles, are valuable for understanding the origin and evolution of the tetrapod brain and spinal cord. Their metamorphic developmental transitions and unique regenerative abilities also facilitate the discovery of mechanisms for neural circuit remodeling and replacement. The genetic toolkit for amphibians, however, remains limited, with only a few species having sequenced genomes and a small number of transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become a powerful alternative to genome modification for visualizing and perturbing the nervous system. AAVs are DNA viruses that enable neuronal transduction in both developing and adult animals with low toxicity and spatial, temporal, and cell-type specificity. However, AAVs have never been shown to transduce amphibian cells efficiently. To bridge this gap, we established a simple, scalable, and robust strategy to screen AAV serotypes in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl, in both developing larval tadpoles and post-metamorphic animals. For each species, we successfully identified at least two AAV serotypes capable of infecting the CNS; however, no pan-amphibian serotype was identified, indicating rapid evolution of AAV tropism. In addition, we developed an AAV-based strategy that targets isochronic cohorts of developing neurons – a critical tool for parsing neural circuit assembly. Finally, to enable visualization and manipulation of neural circuits, we identified AAV variants for retrograde tracing of neuronal projections in adult animals. Our findings expand the toolkit for amphibians to include AAVs, establish a generalizable workflow for AAV screening in non-canonical research organisms, generate testable hypotheses for the evolution of AAV tropism, and lay the foundation for modern cross-species comparisons of vertebrate CNS development, function, and evolution. "}],"project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Entwicklung und Funktion der V1 Interneuronen vom Schwimmen zum Laufen während der Metamorphose von Xenopus"},{"grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"}],"type":"preprint","language":[{"iso":"eng"}],"date_published":"2024-02-16T00:00:00Z","month":"02","publication":"bioRxiv","status":"public","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"publication_status":"submitted","day":"16","date_updated":"2024-02-20T09:34:25Z","year":"2024"},{"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","_id":"15012","publication_identifier":{"isbn":["9783031492716"],"issn":["03029743"],"eissn":["16113349"]},"author":[{"first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János","last_name":"Pach"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"},{"first_name":"Patrick","full_name":"Schnider, Patrick","last_name":"Schnider"}],"publisher":"Springer Nature","type":"conference","scopus_import":"1","volume":14465,"external_id":{"arxiv":["2306.13201"]},"date_published":"2024-01-01T00:00:00Z","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2023-09-22","start_date":"2023-09-20","location":"Isola delle Femmine, Palermo, Italy"},"language":[{"iso":"eng"}],"month":"01","day":"01","date_updated":"2024-02-20T09:13:07Z","date_created":"2024-02-18T23:01:03Z","title":"Decomposition of geometric graphs into star-forests","citation":{"chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In 31st International Symposium on Graph Drawing and Network Visualization, 14465:339–46. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49272-3_23.","ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","apa":"Pach, J., Saghafian, M., & Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49272-3_23","ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14465. Springer Nature; 2024:339-346. doi:10.1007/978-3-031-49272-3_23","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:10.1007/978-3-031-49272-3_23.","short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346."},"alternative_title":["LNCS"],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.13201","open_access":"1"}],"ec_funded":1,"page":"339-346","oa":1,"project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"}],"doi":"10.1007/978-3-031-49272-3_23","abstract":[{"text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"31st International Symposium on Graph Drawing and Network Visualization","intvolume":" 14465","publication_status":"published","department":[{"_id":"HeEd"}],"status":"public","year":"2024"},{"publication_status":"published","department":[{"_id":"KrCh"}],"status":"public","year":"2024","publication":"27th International Conference on Principles of Distributed Systems","intvolume":" 286","oa":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"file":[{"success":1,"date_updated":"2024-02-26T09:04:58Z","content_type":"application/pdf","checksum":"4fc7eea6e4ba140b904781fc7df868ec","file_id":"15028","creator":"dernst","access_level":"open_access","file_name":"2024_LIPICs_Hirvonen.pdf","relation":"main_file","file_size":867363,"date_created":"2024-02-26T09:04:58Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Graphical games are a useful framework for modeling the interactions of (selfish) agents who are connected via an underlying topology and whose behaviors influence each other. They have wide applications ranging from computer science to economics and biology. Yet, even though an agent’s payoff only depends on the actions of their direct neighbors in graphical games, computing the Nash equilibria and making statements about the convergence time of \"natural\" local dynamics in particular can be highly challenging. In this work, we present a novel approach for classifying complexity of Nash equilibria in graphical games by establishing a connection to local graph algorithms, a subfield of distributed computing. In particular, we make the observation that the equilibria of graphical games are equivalent to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable with constant-round local algorithms. This connection allows us to derive novel lower bounds on the convergence time to equilibrium of best-response dynamics in graphical games. Since we establish that distributed convergence can sometimes be provably slow, we also introduce and give bounds on an intuitive notion of \"time-constrained\" inefficiency of best responses. We exemplify how our results can be used in the implementation of mechanisms that ensure convergence of best responses to a Nash equilibrium. Our results thus also give insight into the convergence of strategy-proof algorithms for graphical games, which is still not well understood.","lang":"eng"}],"doi":"10.4230/LIPIcs.OPODIS.2023.11","file_date_updated":"2024-02-26T09:04:58Z","date_created":"2024-02-18T23:01:01Z","title":"On the convergence time in graphical games: A locality-sensitive approach","alternative_title":["LIPIcs"],"citation":{"short":"J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” 27th International Conference on Principles of Distributed Systems, vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.11.","ama":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical games: A locality-sensitive approach. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.11","apa":"Hirvonen, J., Schmid, L., Chatterjee, K., & Schmid, S. (2024). On the convergence time in graphical games: A locality-sensitive approach. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11","ieee":"J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence time in graphical games: A locality-sensitive approach,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","chicago":"Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11.","ista":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time in graphical games: A locality-sensitive approach. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 11."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"day":"18","date_updated":"2024-02-26T09:16:12Z","date_published":"2024-01-18T00:00:00Z","external_id":{"arxiv":["2102.13457"]},"conference":{"location":"Tokyo, Japan","end_date":"2023-12-08","start_date":"2023-12-06","name":"OPODIS: Conference on Principles of Distributed Systems"},"language":[{"iso":"eng"}],"month":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Hirvonen","full_name":"Hirvonen, Juho","first_name":"Juho"},{"orcid":"0000-0002-6978-7329","first_name":"Laura","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"type":"conference","scopus_import":"1","volume":286,"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"This work was partially funded by the Academy of Finland, grant 314888, the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324.","ddc":["000"],"article_number":"11","publication_identifier":{"issn":["18688969"],"isbn":["9783959773089"]},"_id":"15006"},{"issue":"7","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":" 121","publication_status":"published","status":"public","department":[{"_id":"AnSa"}],"year":"2024","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","date_created":"2024-02-18T23:01:00Z","citation":{"mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","ieee":"S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121."},"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"related_material":{"record":[{"id":"15027","status":"public","relation":"research_data"}]},"ec_funded":1,"oa":1,"article_type":"original","file":[{"file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","relation":"main_file","date_created":"2024-02-26T08:20:00Z","file_size":7699487,"creator":"dernst","access_level":"open_access","file_name":"2024_PNAS_Curk.pdf","success":1,"date_updated":"2024-02-26T08:20:00Z","content_type":"application/pdf"}],"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"file_date_updated":"2024-02-26T08:20:00Z","doi":"10.1073/pnas.2220075121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.","lang":"eng"}],"external_id":{"pmid":["38335256"]},"date_published":"2024-02-13T00:00:00Z","language":[{"iso":"eng"}],"month":"02","day":"13","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2024-02-26T08:45:56Z","quality_controlled":"1","pmid":1,"acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","article_processing_charge":"Yes","ddc":["570"],"article_number":"e2220075121","_id":"15001","publication_identifier":{"eissn":["1091-6490"]},"author":[{"id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","full_name":"Curk, Samo","last_name":"Curk","orcid":"0000-0001-6160-9766","first_name":"Samo"},{"last_name":"Krausser","full_name":"Krausser, Johannes","first_name":"Johannes"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":121},{"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","article_number":"050401","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"_id":"15002","publisher":"American Physical Society","author":[{"last_name":"Petrova","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena","first_name":"Elena"},{"first_name":"Egor S.","last_name":"Tiunov","full_name":"Tiunov, Egor S."},{"first_name":"Mari Carmen","full_name":"Bañuls, Mari Carmen","last_name":"Bañuls"},{"first_name":"Aleksey K.","full_name":"Fedorov, Aleksey K.","last_name":"Fedorov"}],"scopus_import":"1","type":"journal_article","volume":132,"date_published":"2024-01-30T00:00:00Z","external_id":{"arxiv":["2201.10220"]},"language":[{"iso":"eng"}],"month":"01","day":"30","date_updated":"2024-02-26T08:03:31Z","title":"Fractal states of the Schwinger model","date_created":"2024-02-18T23:01:00Z","citation":{"chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” Physical Review Letters. American Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401.","ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American Physical Society, 2024.","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal states of the Schwinger model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.132.050401","ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:10.1103/PhysRevLett.132.050401.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024)."},"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.10220"}],"oa":1,"article_type":"original","abstract":[{"text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevLett.132.050401","issue":"5","publication":"Physical Review Letters","intvolume":" 132","publication_status":"published","status":"public","department":[{"_id":"MaSe"}],"year":"2024"},{"day":"02","date_updated":"2024-02-26T09:39:07Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2206.00230"]},"date_published":"2024-02-02T00:00:00Z","month":"02","author":[{"orcid":"0000-0002-9573-2962","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"publisher":"Springer Nature","type":"journal_article","scopus_import":"1","article_processing_charge":"No","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) . The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","quality_controlled":"1","_id":"12485","publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"status":"public","department":[{"_id":"JuFi"}],"publication_status":"epub_ahead","year":"2024","publication":"Probability Theory and Related Fields","article_type":"original","oa":1,"doi":"10.1007/s00440-023-01249-x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"citation":{"ama":"Agresti A, Veraar M. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01249-x","mla":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01249-x.","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024).","chicago":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01249-x.","ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields.","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","apa":"Agresti, A., & Veraar, M. (2024). The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01249-x"},"title":"The critical variational setting for stochastic evolution equations","date_created":"2023-02-02T10:45:15Z","main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"ec_funded":1,"oa_version":"Preprint"},{"year":"2024","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published","intvolume":" 287","publication":"15th Innovations in Theoretical Computer Science Conference","abstract":[{"lang":"eng","text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-26T10:10:48Z","doi":"10.4230/LIPIcs.ITCS.2024.55","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"file":[{"checksum":"b89716aae6a5599f187897e39de1e53a","file_id":"15030","access_level":"open_access","file_name":"2024_LIPICs_Goranci.pdf","creator":"dernst","date_created":"2024-02-26T10:10:48Z","file_size":1054754,"relation":"main_file","date_updated":"2024-02-26T10:10:48Z","success":1,"content_type":"application/pdf"}],"oa":1,"ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ieee":"G. Goranci, M. H. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287.","apa":"Goranci, G., Henzinger, M. H., Räcke, H., Sachdeva, S., & Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.55","ista":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 287, 55.","chicago":"Goranci, Gramoz, Monika H Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In 15th Innovations in Theoretical Computer Science Conference, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.","short":"G. Goranci, M.H. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55.","ama":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55"},"alternative_title":["LIPIcs"],"date_created":"2024-02-18T23:01:02Z","title":"Electrical flows for polylogarithmic competitive oblivious routing","date_updated":"2024-02-26T10:12:19Z","day":"24","month":"01","conference":{"location":"Berkeley, CA, United States","end_date":"2024-02-02","start_date":"2024-01-30","name":"ITCS: Innovations in Theoretical Computer Science Conference"},"language":[{"iso":"eng"}],"date_published":"2024-01-24T00:00:00Z","external_id":{"arxiv":["2303.02491"]},"volume":287,"has_accepted_license":"1","type":"conference","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Goranci","full_name":"Goranci, Gramoz","first_name":"Gramoz"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"first_name":"Sushant","full_name":"Sachdeva, Sushant","last_name":"Sachdeva"},{"first_name":"A. R.","last_name":"Sricharan","full_name":"Sricharan, A. R."}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"_id":"15008","ddc":["000"],"article_number":"55","acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","article_processing_charge":"No","quality_controlled":"1"},{"month":"01","conference":{"name":"OPODIS: Conference on Principles of Distributed Systems","start_date":"2023-12-06","end_date":"2023-12-08","location":"Tokyo, Japan"},"language":[{"iso":"eng"}],"date_published":"2024-01-18T00:00:00Z","external_id":{"arxiv":["2307.02954"]},"date_updated":"2024-02-26T10:18:18Z","day":"18","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773089"]},"_id":"15007","ddc":["000"],"article_number":"12","article_processing_charge":"No","acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","quality_controlled":"1","has_accepted_license":"1","volume":286,"type":"conference","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Orestis","full_name":"Alpos, Orestis","last_name":"Alpos"},{"full_name":"Amores-Sesar, Ignacio","last_name":"Amores-Sesar","first_name":"Ignacio"},{"full_name":"Cachin, Christian","last_name":"Cachin","first_name":"Christian"},{"first_name":"Michelle X","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"}],"intvolume":" 286","publication":"27th International Conference on Principles of Distributed Systems","year":"2024","department":[{"_id":"KrPi"}],"status":"public","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"apa":"Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12.","chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12.","mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” 27th International Conference on Principles of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12.","short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12"},"alternative_title":["LIPIcs"],"date_created":"2024-02-18T23:01:02Z","title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","abstract":[{"text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-02-26T10:16:57Z","doi":"10.4230/LIPIcs.OPODIS.2023.12","file":[{"relation":"main_file","file_size":1505994,"date_created":"2024-02-26T10:16:57Z","creator":"dernst","file_name":"2024_LIPICs_Alpos.pdf","access_level":"open_access","file_id":"15031","checksum":"2993e810a45e8c8056106834b07aea92","content_type":"application/pdf","success":1,"date_updated":"2024-02-26T10:16:57Z"}],"oa":1},{"article_processing_charge":"No","acknowledgement":"This project has received funding from the Euro-pean Research Council (ERC) under the EuropeanUnion’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The De-sign of Modern Fully Dynamic Data Structures (Mo-DynStruct)” and the Austrian Science Fund (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical Graph Decompositions”, I 5982-N, and project“Fast Algorithms for a Reactive Network Layer (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D. Sauplic has received funding from the Euro-pean Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreementNo 101034413.","quality_controlled":"1","_id":"14769","publication_identifier":{"eisbn":["9781611977929"]},"author":[{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"last_name":"Saulpic","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David","first_name":"David"},{"first_name":"Leonhard","id":"8b563fd0-b441-11ee-9101-a3891c61efa6","full_name":"Sidl, Leonhard","last_name":"Sidl"}],"publisher":"Society for Industrial & Applied Mathematics","type":"conference","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2024-01-08","start_date":"2024-01-07","name":"ALENEX: Workshop on Algorithm Engineering and Experiments","location":"Alexandria, VA, United States"},"external_id":{"arxiv":["2310.18034"]},"date_published":"2024-01-04T00:00:00Z","month":"01","day":"04","date_updated":"2024-02-26T09:51:31Z","citation":{"ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. Society for Industrial & Applied Mathematics; 2024:220-233. doi:10.1137/1.9781611977929.17","mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–33, doi:10.1137/1.9781611977929.17.","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–233.","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, 220–33. Society for Industrial & Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977929.17.","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","apa":"Henzinger, M. H., Saulpic, D., & Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments (pp. 220–233). Alexandria, VA, United States: Society for Industrial & Applied Mathematics. https://doi.org/10.1137/1.9781611977929.17","ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Alexandria, VA, United States, 2024, pp. 220–233."},"date_created":"2024-01-09T16:22:47Z","title":"Experimental evaluation of fully dynamic k-means via coresets","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18034"}],"ec_funded":1,"oa_version":"Preprint","oa":1,"page":"220-233","doi":"10.1137/1.9781611977929.17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.","lang":"eng"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published","year":"2024"},{"date_updated":"2024-02-26T09:59:30Z","day":"20","month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-20T00:00:00Z","external_id":{"pmid":["38245839"]},"volume":16,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Oxford University Press","author":[{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"publication_identifier":{"eissn":["1759-6653"]},"_id":"15009","ddc":["570"],"article_number":"evae006","article_processing_charge":"Yes","pmid":1,"quality_controlled":"1","year":"2024","status":"public","department":[{"_id":"BeVi"}],"publication_status":"published","intvolume":" 16","publication":"Genome Biology and Evolution","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"doi":"10.1093/gbe/evae006","file_date_updated":"2024-02-26T09:54:59Z","file":[{"file_size":5213306,"date_created":"2024-02-26T09:54:59Z","relation":"main_file","file_name":"2024_GBE_Bett.pdf","access_level":"open_access","creator":"dernst","file_id":"15029","checksum":"106a40f10443b2e7ba66749844ebbdf1","content_type":"application/pdf","date_updated":"2024-02-26T09:54:59Z","success":1}],"article_type":"original","oa":1,"related_material":{"record":[{"relation":"research_data","id":"14705","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006","apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006."},"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","date_created":"2024-02-18T23:01:02Z"},{"issue":"2","publication":"Physical Review A","intvolume":" 109","publication_status":"published","department":[{"_id":"MiLe"}],"status":"public","year":"2024","title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","date_created":"2024-02-18T23:01:01Z","citation":{"mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 2024;109(2). doi:10.1103/PhysRevA.109.023101","apa":"Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” Physical Review A, vol. 109, no. 2. American Physical Society, 2024.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.","ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101."},"oa_version":"Preprint","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"oa":1,"article_type":"original","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"abstract":[{"text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevA.109.023101","date_published":"2024-02-01T00:00:00Z","external_id":{"arxiv":["2307.07256"]},"language":[{"iso":"eng"}],"month":"02","day":"01","date_updated":"2024-02-26T09:45:20Z","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","article_number":"023101","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"_id":"15004","publisher":"American Physical Society","author":[{"first_name":"Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"scopus_import":"1","type":"journal_article","volume":109},{"date_updated":"2024-02-26T09:59:29Z","year":"2024","day":"02","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"month":"01","date_published":"2024-01-02T00:00:00Z","file":[{"file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca","date_created":"2023-12-22T13:54:21Z","file_size":847,"relation":"main_file","access_level":"open_access","file_name":"readme.txt.txt","creator":"melkrewi","date_updated":"2023-12-22T13:54:21Z","success":1,"content_type":"text/plain"},{"file_id":"14708","checksum":"973e1cbdab923a71709782177980829f","date_created":"2023-12-22T14:14:06Z","file_size":343632753,"relation":"main_file","file_name":"data_artemia_franciscana_genome.zip","access_level":"open_access","creator":"melkrewi","date_updated":"2023-12-22T14:14:06Z","success":1,"content_type":"application/x-zip-compressed"}],"project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"type":"research_data","file_date_updated":"2023-12-22T14:14:06Z","doi":"10.15479/AT:ISTA:14705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"has_accepted_license":"1","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"}],"oa":1,"publisher":"Institute of Science and Technology Austria","contributor":[{"first_name":"Vincent K","contributor_type":"researcher","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"contributor_type":"project_member","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"orcid":"0000-0002-5328-7231","contributor_type":"researcher","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"ddc":["576"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15009"}]},"_id":"14705","date_created":"2023-12-22T13:40:48Z","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","citation":{"ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705.","short":"M.N. Elkrewi, (2024).","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705"},"article_processing_charge":"No"},{"author":[{"full_name":"Shimura, Yosuke","last_name":"Shimura","first_name":"Yosuke"},{"first_name":"Clement","full_name":"Godfrin, Clement","last_name":"Godfrin"},{"first_name":"Andriy","last_name":"Hikavyy","full_name":"Hikavyy, Andriy"},{"last_name":"Li","full_name":"Li, Roy","first_name":"Roy"},{"orcid":"0000-0002-2862-8372","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"},{"full_name":"Favia, Paola","last_name":"Favia","first_name":"Paola"},{"first_name":"Han","full_name":"Han, Han","last_name":"Han"},{"first_name":"Danny","full_name":"Wan, Danny","last_name":"Wan"},{"last_name":"de Greve","full_name":"de Greve, Kristiaan","first_name":"Kristiaan"},{"full_name":"Loo, Roger","last_name":"Loo","first_name":"Roger"}],"publisher":"Elsevier","volume":174,"has_accepted_license":"1","type":"journal_article","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","article_processing_charge":"No","quality_controlled":"1","_id":"15018","publication_identifier":{"issn":["1369-8001"]},"ddc":["530"],"article_number":"108231","day":"20","date_updated":"2024-02-26T10:36:35Z","language":[{"iso":"eng"}],"date_published":"2024-02-20T00:00:00Z","month":"02","article_type":"original","oa":1,"doi":"10.1016/j.mssp.2024.108231","abstract":[{"lang":"eng","text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated GermaNIum quanTum tEchnology"}],"citation":{"short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231."},"title":"Compressively strained epitaxial Ge layers for quantum computing applications","date_created":"2024-02-22T14:10:40Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.mssp.2024.108231"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"status":"public","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"publication_status":"epub_ahead","year":"2024","issue":"5","intvolume":" 174","publication":"Materials Science in Semiconductor Processing"},{"date_created":"2024-02-18T23:01:03Z","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","citation":{"short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research, vol. 234, ML Research Press, 2024, pp. 542–53.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning Research. Vol 234. ML Research Press; 2024:542-553.","apa":"Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In Proceedings of Machine Learning Research, 234:542–53. ML Research Press, 2024."},"alternative_title":["PMLR"],"oa_version":"Preprint","main_file_link":[{"url":"https://proceedings.mlr.press/v234/kurtic24a","open_access":"1"}],"page":"542-553","oa":1,"abstract":[{"lang":"eng","text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of Machine Learning Research","intvolume":" 234","publication_status":"published","status":"public","department":[{"_id":"DaAl"}],"year":"2024","quality_controlled":"1","article_processing_charge":"No","_id":"15011","publication_identifier":{"eissn":["2640-3498"]},"author":[{"full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","last_name":"Kurtic","first_name":"Eldar"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"publisher":"ML Research Press","type":"conference","scopus_import":"1","volume":234,"external_id":{"arxiv":["2312.13547"]},"date_published":"2024-01-08T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Hongkong, China","name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-06","start_date":"2024-01-03"},"month":"01","day":"08","date_updated":"2024-02-26T10:30:52Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"date_created":"2024-02-25T23:00:55Z","title":"Correlation-induced viscous dissipation in concentrated electrolytes","citation":{"mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215."},"file":[{"content_type":"application/pdf","success":1,"date_updated":"2024-02-27T08:12:52Z","creator":"dernst","file_name":"2024_JourChemicalPhysics_Robin.pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-27T08:12:52Z","file_size":5452738,"checksum":"0a5e0ae70849bce674466fc054390ec0","file_id":"15034"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"abstract":[{"text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1063/5.0188215","file_date_updated":"2024-02-27T08:12:52Z","oa":1,"article_type":"original","publication":"Journal of Chemical Physics","intvolume":" 160","issue":"6","year":"2024","publication_status":"published","status":"public","department":[{"_id":"EdHa"}],"ddc":["540"],"article_number":"064503","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"_id":"15024","quality_controlled":"1","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","article_processing_charge":"Yes (in subscription journal)","pmid":1,"scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":160,"publisher":"AIP Publishing","author":[{"id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","full_name":"Robin, Paul","last_name":"Robin","orcid":"0000-0002-5728-9189","first_name":"Paul"}],"month":"02","date_published":"2024-02-14T00:00:00Z","external_id":{"pmid":["38349632"],"arxiv":["2311.11784"]},"language":[{"iso":"eng"}],"date_updated":"2024-02-27T08:16:06Z","day":"14"},{"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","publication_identifier":{"issn":["1050-5164"]},"_id":"15025","publisher":"Institute of Mathematical Statistics","author":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László"},{"first_name":"Benjamin","orcid":"0000-0003-2625-495X","last_name":"McKenna","full_name":"McKenna, Benjamin","id":"b0cc634c-d549-11ee-96c8-87338c7ad808"}],"type":"journal_article","scopus_import":"1","volume":34,"date_published":"2024-02-01T00:00:00Z","external_id":{"arxiv":["2208.12206"]},"language":[{"iso":"eng"}],"month":"02","day":"01","date_updated":"2024-02-27T08:29:05Z","date_created":"2024-02-25T23:00:56Z","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","citation":{"ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000.","apa":"Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AAP2000","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000."},"oa_version":"Preprint","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.12206"}],"page":"1623-1662","article_type":"original","oa":1,"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble.","lang":"eng"}],"doi":"10.1214/23-AAP2000","issue":"1B","publication":"Annals of Applied Probability","intvolume":" 34","publication_status":"published","department":[{"_id":"LaEr"}],"status":"public","year":"2024"},{"volume":13,"has_accepted_license":"1","type":"journal_article","publisher":"eLife Sciences Publications","author":[{"orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski"},{"first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"publication_identifier":{"issn":["2050-084X"]},"_id":"15033","ddc":["580"],"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","article_processing_charge":"Yes","quality_controlled":"1","date_updated":"2024-02-28T12:29:43Z","day":"21","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-21T00:00:00Z","abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.7554/elife.68993","project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"oa":1,"article_type":"original","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993."},"date_created":"2024-02-27T07:10:11Z","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","year":"2024","department":[{"_id":"JiFr"}],"status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publication_status":"epub_ahead","intvolume":" 13","publication":"eLife"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"oa_version":"Preprint","citation":{"mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017."},"title":"Fungal infection alters collective nutritional intake of ant colonies","date_created":"2023-10-31T13:30:20Z","abstract":[{"lang":"eng","text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.cub.2024.01.017","oa":1,"article_type":"original","page":"902-909.e6","intvolume":" 34","publication":"Current Biology","issue":"4","year":"2024","status":"public","department":[{"_id":"SyCr"}],"publication_status":"published","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"_id":"14479","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","article_processing_charge":"No","pmid":1,"quality_controlled":"1","volume":34,"type":"journal_article","scopus_import":"1","publisher":"Elsevier","author":[{"last_name":"Csata","full_name":"Csata, Eniko","first_name":"Eniko"},{"first_name":"Alfonso","full_name":"Perez-Escudero, Alfonso","last_name":"Perez-Escudero"},{"first_name":"Emmanuel","last_name":"Laury","full_name":"Laury, Emmanuel"},{"first_name":"Hanna","full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","last_name":"Leitner"},{"full_name":"Latil, Gerard","last_name":"Latil","first_name":"Gerard"},{"last_name":"Heinze","full_name":"Heinze, Juerge","first_name":"Juerge"},{"first_name":"Stephen","full_name":"Simpson, Stephen","last_name":"Simpson"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"},{"first_name":"Audrey","last_name":"Dussutour","full_name":"Dussutour, Audrey"}],"month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-26T00:00:00Z","external_id":{"pmid":["38307022"]},"date_updated":"2024-03-04T07:14:41Z","day":"26"},{"month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-17T00:00:00Z","external_id":{"arxiv":["2401.08454"]},"date_updated":"2024-03-04T07:08:16Z","day":"17","publication_identifier":{"issn":["1432-5411"]},"_id":"15045","ddc":["530"],"article_number":"12","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","volume":65,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Springer Nature","author":[{"first_name":"Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"},{"orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"intvolume":" 65","publication":"Few-Body Systems","year":"2024","status":"public","department":[{"_id":"MiLe"}],"keyword":["Atomic and Molecular Physics","and Optics"],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024.","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x"},"date_created":"2024-03-01T11:39:33Z","title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00601-024-01880-x","file_date_updated":"2024-03-04T07:07:10Z","file":[{"file_name":"2024_FewBodySys_Varshney.pdf","access_level":"open_access","creator":"dernst","file_size":436712,"date_created":"2024-03-04T07:07:10Z","relation":"main_file","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_id":"15049","content_type":"application/pdf","date_updated":"2024-03-04T07:07:10Z","success":1}],"article_type":"original","oa":1},{"issue":"1","intvolume":" 6","publication":"Physical Review Research","department":[{"_id":"MiLe"}],"status":"public","keyword":["General Physics and Astronomy"],"publication_status":"published","year":"2024","citation":{"chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024)."},"title":"Multipurpose platform for analog quantum simulation","date_created":"2024-03-04T07:42:52Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","article_type":"original","oa":1,"abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-03-04T07:53:08Z","doi":"10.1103/physrevresearch.6.013158","file":[{"relation":"main_file","file_size":4025988,"date_created":"2024-03-04T07:53:08Z","creator":"dernst","file_name":"2024_PhysicalReviewResearch_Jin.pdf","access_level":"open_access","file_id":"15054","checksum":"ba2ae3e3a011f8897d3803c9366a67e2","content_type":"application/pdf","success":1,"date_updated":"2024-03-04T07:53:08Z"}],"language":[{"iso":"eng"}],"date_published":"2024-02-13T00:00:00Z","external_id":{"arxiv":["2304.08433"]},"month":"02","day":"13","date_updated":"2024-03-04T07:55:29Z","article_processing_charge":"Yes","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"_id":"15053","article_number":"013158","ddc":["530"],"publisher":"American Physical Society","author":[{"first_name":"Shuwei","last_name":"Jin","full_name":"Jin, Shuwei"},{"last_name":"Dai","full_name":"Dai, Kunlun","first_name":"Kunlun"},{"first_name":"Joris","last_name":"Verstraten","full_name":"Verstraten, Joris"},{"first_name":"Maxime","full_name":"Dixmerias, Maxime","last_name":"Dixmerias"},{"first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"full_name":"Salomon, Christophe","last_name":"Salomon","first_name":"Christophe"},{"last_name":"Peaudecerf","full_name":"Peaudecerf, Bruno","first_name":"Bruno"},{"first_name":"Tim","full_name":"de Jongh, Tim","last_name":"de Jongh"},{"full_name":"Yefsah, Tarik","last_name":"Yefsah","first_name":"Tarik"}],"volume":6,"has_accepted_license":"1","type":"journal_article","scopus_import":"1"},{"day":"01","date_updated":"2024-03-04T07:28:25Z","language":[{"iso":"eng"}],"date_published":"2024-02-01T00:00:00Z","month":"02","publisher":"The Company of Biologists","author":[{"last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","orcid":"0000-0001-7659-9142"},{"first_name":"Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"has_accepted_license":"1","volume":151,"type":"journal_article","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","quality_controlled":"1","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"_id":"15048","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"status":"public","publication_status":"published","year":"2024","issue":"4","intvolume":" 151","publication":"Development","article_type":"original","oa":1,"page":"1-18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-03-04T07:24:43Z","doi":"10.1242/dev.202316","file":[{"date_created":"2024-03-04T07:24:43Z","file_size":14839986,"relation":"main_file","file_name":"2024_Development_Schauer.pdf","access_level":"open_access","creator":"dernst","file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","content_type":"application/pdf","date_updated":"2024-03-04T07:24:43Z","success":1}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"citation":{"ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024."},"date_created":"2024-03-03T23:00:50Z","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","ec_funded":1,"related_material":{"record":[{"id":"14926","status":"public","relation":"research_data"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"month":"02","date_published":"2024-02-02T00:00:00Z","year":"2024","date_updated":"2024-03-04T07:28:25Z","license":"https://opensource.org/licenses/MIT","department":[{"_id":"Bio"}],"status":"public","day":"02","_id":"14926","related_material":{"record":[{"relation":"used_in_publication","id":"15048","status":"public"}]},"tmp":{"short":"MIT","legal_code_url":"https://opensource.org/licenses/MIT","name":"The MIT License"},"ddc":["570"],"citation":{"ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","short":"R. Hauschild, (2024).","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926.","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926"},"title":"Matlab script for analysis of clone dispersal","date_created":"2024-02-02T14:42:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.15479/AT:ISTA:14926","file_date_updated":"2024-02-02T14:40:31Z","type":"software","file":[{"content_type":"application/octet-stream","success":1,"date_updated":"2024-02-02T14:40:31Z","relation":"main_file","file_size":736,"date_created":"2024-02-02T14:40:31Z","creator":"rhauschild","file_name":"README.md","access_level":"open_access","file_id":"14927","checksum":"df7f358ae19a176cf710c0a802ce31b1"},{"relation":"main_file","file_size":3543,"date_created":"2024-02-02T14:40:31Z","creator":"rhauschild","file_name":"Supplementary_file_1.zip","access_level":"open_access","file_id":"14928","checksum":"10194cc11619eccd8f4b24472e465b7f","content_type":"application/x-zip-compressed","success":1,"date_updated":"2024-02-02T14:40:31Z"}],"publisher":"ISTA","author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert"}],"oa":1},{"day":"23","date_updated":"2024-03-05T09:26:47Z","language":[{"iso":"eng"}],"date_published":"2024-02-23T00:00:00Z","external_id":{"pmid":["38394192"]},"month":"02","publisher":"American Association for the Advancement of Science","author":[{"first_name":"Jiawei","last_name":"Bao","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei"},{"last_name":"Stevens","full_name":"Stevens, Bjorn","first_name":"Bjorn"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"}],"has_accepted_license":"1","volume":10,"scopus_import":"1","type":"journal_article","article_processing_charge":"Yes","acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","pmid":1,"quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"_id":"15047","article_number":"eadj6801","ddc":["550"],"department":[{"_id":"CaMu"}],"status":"public","publication_status":"published","year":"2024","issue":"8","intvolume":" 10","publication":"Science Advances","oa":1,"article_type":"original","abstract":[{"text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1126/sciadv.adj6801","file_date_updated":"2024-03-04T07:34:00Z","file":[{"date_updated":"2024-03-04T07:34:00Z","success":1,"content_type":"application/pdf","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_id":"15051","file_name":"2024_ScienceAdv_Bao.pdf","access_level":"open_access","creator":"dernst","file_size":800926,"date_created":"2024-03-04T07:34:00Z","relation":"main_file"}],"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","call_identifier":"H2020"}],"citation":{"chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024)."},"date_created":"2024-03-03T23:00:50Z","title":"Intensification of daily tropical precipitation extremes from more organized convection","ec_funded":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"month":"01","external_id":{"pmid":["38096816"]},"date_published":"2024-01-17T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2024-03-05T09:43:02Z","day":"17","ddc":["570"],"_id":"12875","publication_identifier":{"issn":["0896-6273"]},"quality_controlled":"1","pmid":1,"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","article_processing_charge":"Yes (via OA deal)","type":"journal_article","scopus_import":"1","volume":112,"has_accepted_license":"1","author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner"},{"last_name":"Krausgruber","full_name":"Krausgruber, Thomas","first_name":"Thomas"},{"first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"full_name":"Schrammel, Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel","first_name":"Martin"},{"first_name":"Natalie Y","last_name":"Özgen","full_name":"Özgen, Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"first_name":"Alexis","last_name":"Ivec","full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"publisher":"Elsevier","publication":"Neuron","intvolume":" 112","issue":"2","year":"2024","publication_status":"published","department":[{"_id":"SiHi"},{"_id":"RySh"}],"status":"public","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","description":"News on ISTA Website","relation":"press_release"}]},"date_created":"2023-04-27T09:41:48Z","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","citation":{"short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11."},"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"}],"file":[{"date_updated":"2024-02-06T13:56:15Z","success":1,"content_type":"application/pdf","checksum":"32b3788f7085cf44a84108d8faaff3ce","file_id":"14944","access_level":"open_access","file_name":"2024_Neuron_Cheung.pdf","creator":"dernst","file_size":5942467,"date_created":"2024-02-06T13:56:15Z","relation":"main_file"}],"file_date_updated":"2024-02-06T13:56:15Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2023.11.009","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"page":"230-246.e11","article_type":"original","oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1038/s41594-023-01201-6","project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"oa":1,"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01201-6"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024."},"date_created":"2024-02-12T09:59:45Z","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","year":"2024","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","keyword":["Molecular Biology","Structural Biology"],"publication_status":"epub_ahead","publication":"Nature Structural & Molecular Biology","has_accepted_license":"1","type":"journal_article","publisher":"Springer Nature","author":[{"last_name":"Datler","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0002-3616-8580"},{"first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse"},{"last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","first_name":"Andreas"},{"first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas W","last_name":"Bauer","full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"_id":"14979","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","pmid":1,"quality_controlled":"1","date_updated":"2024-03-05T09:27:47Z","day":"05","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-05T00:00:00Z","external_id":{"pmid":["38316877"]}},{"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"_id":"14846","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","quality_controlled":"1","has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Springer Nature","author":[{"orcid":"0000-0002-5223-3346","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo"},{"first_name":"Rushikesh","full_name":"Shinde, Rushikesh","last_name":"Shinde"},{"orcid":"0000-0002-8176-4824","first_name":"Madison","full_name":"Bolger-Munro, Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","last_name":"Bolger-Munro"},{"first_name":"Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gregory","full_name":"Szep, Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","last_name":"Szep"},{"last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene","first_name":"Irene"},{"full_name":"Labrousse Arias, David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","last_name":"Labrousse Arias","first_name":"David"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","orcid":"0000-0002-9438-4783","first_name":"Vanessa"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","last_name":"Merrin"},{"full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones","first_name":"Andrew"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"month":"01","language":[{"iso":"eng"}],"date_published":"2024-01-09T00:00:00Z","date_updated":"2024-03-05T09:33:38Z","day":"09","main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024."},"date_created":"2024-01-21T23:00:57Z","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"doi":"10.1038/s41567-023-02302-1","project":[{"name":"Control of embryonic cleavage pattern","grant_number":"I03601","call_identifier":"FWF","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"article_type":"original","oa":1,"publication":"Nature Physics","year":"2024","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"status":"public","publication_status":"epub_ahead"},{"day":"23","date_updated":"2024-03-06T14:22:52Z","date_published":"2024-02-23T00:00:00Z","language":[{"iso":"eng"}],"month":"02","author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","has_accepted_license":"1","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"article_processing_charge":"No","ddc":["576","519"],"_id":"15020","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","keyword":["Theoretical biology","Optimality","Evolution","Information"],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","year":"2024","page":"158","oa":1,"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"file":[{"date_updated":"2024-02-23T13:50:53Z","success":1,"content_type":"application/pdf","file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","file_size":7102089,"date_created":"2024-02-23T13:50:53Z","relation":"main_file","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access","creator":"mhledik"},{"creator":"mhledik","file_name":"hledik thesis source.zip","access_level":"closed","relation":"source_file","date_created":"2024-02-23T13:50:54Z","file_size":14014790,"checksum":"eda9b9430da2610fee7ce1c1419a479a","file_id":"15022","content_type":"application/zip","date_updated":"2024-02-23T14:20:16Z"}],"file_date_updated":"2024-02-23T14:20:16Z","acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:15020","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Genetic information and biological optimization","date_created":"2024-02-23T14:02:04Z","alternative_title":["ISTA Thesis"],"citation":{"apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020"},"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7553","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12081","status":"public"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1},{"department":[{"_id":"EvBe"}],"status":"public","publication_status":"published","year":"2024","issue":"1","intvolume":" 34","publication":"Current Biology","oa":1,"page":"R3-R5","doi":"10.1016/j.cub.2023.11.039","abstract":[{"text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.","short":"E. Benková, Eva Benkova, Elsevier, 2024."},"title":"Eva Benkova","date_created":"2024-01-21T23:00:56Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"oa_version":"Published Version","day":"08","date_updated":"2024-03-12T12:19:12Z","language":[{"iso":"eng"}],"date_published":"2024-01-08T00:00:00Z","month":"01","author":[{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"publisher":"Elsevier","volume":34,"type":"other_academic_publication","article_processing_charge":"No","quality_controlled":"1","_id":"14842","publication_identifier":{"eissn":["1879-0445"]}},{"volume":121,"has_accepted_license":"1","type":"journal_article","publisher":"Proceedings of the National Academy of Sciences","author":[{"orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"first_name":"Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier"},{"full_name":"Roy, Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","last_name":"Roy","first_name":"Utsa"},{"first_name":"Yukihiro","last_name":"Nakamura","full_name":"Nakamura, Yukihiro"},{"first_name":"Tetsushi","full_name":"Sadakata, Tetsushi","last_name":"Sadakata"},{"first_name":"Makoto","last_name":"Sanbo","full_name":"Sanbo, Makoto"},{"last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi","first_name":"Masumi"},{"full_name":"Rhee, JeongSeop","last_name":"Rhee","first_name":"JeongSeop"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"15084","article_number":"e2301449121","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","pmid":1,"quality_controlled":"1","date_updated":"2024-03-12T13:44:18Z","day":"20","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-20T00:00:00Z","external_id":{"pmid":["38346189"]},"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"file_date_updated":"2024-03-12T13:42:42Z","doi":"10.1073/pnas.2301449121","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file":[{"success":1,"date_updated":"2024-03-12T13:42:42Z","content_type":"application/pdf","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_id":"15110","creator":"dernst","access_level":"open_access","file_name":"2024_PNAS_Koppensteiner.pdf","relation":"main_file","file_size":13648221,"date_created":"2024-03-12T13:42:42Z"}],"oa":1,"article_type":"original","ec_funded":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}],"record":[{"status":"public","id":"13173","relation":"research_data"}]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","citation":{"ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024."},"date_created":"2024-03-05T09:23:55Z","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","year":"2024","department":[{"_id":"RySh"},{"_id":"PeJo"}],"status":"public","publication_status":"published","intvolume":" 121","publication":"Proceedings of the National Academy of Sciences","issue":"8"},{"day":"05","date_updated":"2024-03-12T13:29:25Z","language":[{"iso":"eng"}],"date_published":"2024-03-05T00:00:00Z","external_id":{"pmid":["38408249"]},"month":"03","publisher":"Proceedings of the National Academy of Sciences","author":[{"last_name":"Hübner","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","full_name":"Hübner, Valentin","first_name":"Valentin"},{"full_name":"Staab, Manuel","last_name":"Staab","first_name":"Manuel"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"}],"has_accepted_license":"1","volume":121,"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","pmid":1,"quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"15083","ddc":["000"],"article_number":"e2315558121","department":[{"_id":"KrCh"}],"status":"public","publication_status":"published","year":"2024","issue":"10","intvolume":" 121","publication":"Proceedings of the National Academy of Sciences","article_type":"original","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"doi":"10.1073/pnas.2315558121","file_date_updated":"2024-03-12T13:12:22Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":2203220,"date_created":"2024-03-12T13:12:22Z","relation":"main_file","access_level":"open_access","file_name":"2024_PNAS_Huebner.pdf","creator":"dernst","file_id":"15109","checksum":"068520e3efd4d008bb9177e8aedb7d22","content_type":"application/pdf","date_updated":"2024-03-12T13:12:22Z","success":1}],"citation":{"chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121."},"date_created":"2024-03-05T09:18:49Z","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"15108","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","relation":"press_release","description":"News on ISTA Website"}]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version"},{"day":"09","department":[{"_id":"KrCh"}],"status":"public","year":"2024","date_updated":"2024-03-12T13:29:26Z","date_published":"2024-02-09T00:00:00Z","month":"02","publisher":"Zenodo","oa":1,"author":[{"last_name":"Hübner","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","full_name":"Hübner, Valentin","first_name":"Valentin"},{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.5281/ZENODO.10639167","title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","date_created":"2024-03-12T13:02:58Z","article_processing_charge":"No","citation":{"chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","short":"V. Hübner, M. Kleshnina, (2024).","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["000"],"oa_version":"Published Version","_id":"15108","main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"related_material":{"record":[{"relation":"used_in_publication","id":"15083","status":"public"}]}},{"file":[{"file_id":"15111","checksum":"270d2340402729b0532f7072ea914cae","relation":"main_file","file_size":13364601,"date_created":"2024-03-13T08:59:21Z","creator":"dernst","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","access_level":"open_access","success":1,"date_updated":"2024-03-13T08:59:21Z","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study."}],"doi":"10.5194/gmd-17-1563-2024","file_date_updated":"2024-03-13T08:59:21Z","page":"1563-1584","oa":1,"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","date_created":"2024-03-10T23:00:53Z","citation":{"ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024."},"year":"2024","publication_status":"published","status":"public","department":[{"_id":"CaMu"}],"publication":"Geoscientific Model Development","intvolume":" 17","issue":"4","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":17,"publisher":"European Geosciences Union","author":[{"full_name":"Schmidt, Hauke","last_name":"Schmidt","first_name":"Hauke"},{"first_name":"Sebastian","last_name":"Rast","full_name":"Rast, Sebastian"},{"first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei","last_name":"Bao"},{"first_name":"Amrit","full_name":"Cassim, Amrit","last_name":"Cassim"},{"last_name":"Fang","full_name":"Fang, Shih Wei","first_name":"Shih Wei"},{"last_name":"Jimenez-De La Cuesta","full_name":"Jimenez-De La Cuesta, Diego","first_name":"Diego"},{"first_name":"Paul","full_name":"Keil, Paul","last_name":"Keil"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"full_name":"Kroll, Clarissa","last_name":"Kroll","first_name":"Clarissa"},{"last_name":"Lang","full_name":"Lang, Theresa","first_name":"Theresa"},{"last_name":"Niemeier","full_name":"Niemeier, Ulrike","first_name":"Ulrike"},{"last_name":"Schneidereit","full_name":"Schneidereit, Andrea","first_name":"Andrea"},{"full_name":"Williams, Andrew I.L.","last_name":"Williams","first_name":"Andrew I.L."},{"last_name":"Stevens","full_name":"Stevens, Bjorn","first_name":"Bjorn"}],"ddc":["550"],"publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"_id":"15097","quality_controlled":"1","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","article_processing_charge":"Yes (via OA deal)","date_updated":"2024-03-13T09:01:20Z","day":"22","month":"02","date_published":"2024-02-22T00:00:00Z","language":[{"iso":"eng"}]},{"has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Cambridge University Press","author":[{"first_name":"Bartosz","last_name":"Naskręcki","full_name":"Naskręcki, Bartosz"},{"last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo","first_name":"Matteo","orcid":"0000-0002-0854-0306"}],"publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"_id":"12311","ddc":["510"],"article_number":"2203.02015","article_processing_charge":"Yes (via OA deal)","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","quality_controlled":"1","date_updated":"2024-03-13T11:55:21Z","day":"26","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-26T00:00:00Z","external_id":{"arxiv":["2203.02015"]},"abstract":[{"text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1017/prm.2024.7","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_type":"original","oa":1,"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2024.7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7"},"title":"Common valuations of division polynomials","date_created":"2023-01-16T11:45:22Z","year":"2024","status":"public","department":[{"_id":"TiBr"}],"keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"publication_status":"epub_ahead","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics"},{"day":"22","date_updated":"2024-03-13T12:08:57Z","language":[{"iso":"eng"}],"external_id":{"pmid":["38395682"]},"date_published":"2024-02-22T00:00:00Z","month":"02","author":[{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"}],"publisher":"Cell Press","has_accepted_license":"1","type":"journal_article","scopus_import":"1","pmid":1,"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","quality_controlled":"1","_id":"15099","publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"ddc":["570"],"status":"public","department":[{"_id":"NiBa"}],"publication_status":"epub_ahead","year":"2024","publication":"Trends in Genetics","oa":1,"article_type":"review","doi":"10.1016/j.tig.2024.01.002","abstract":[{"text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024)."},"date_created":"2024-03-10T23:00:54Z","title":"Diverse pathways to speciation revealed by marine snails","main_file_link":[{"url":"https://doi.org/10.1016/j.tig.2024.01.002","open_access":"1"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-27T00:00:00Z","external_id":{"arxiv":["2306.11081"]},"date_updated":"2024-03-13T12:20:23Z","day":"27","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"_id":"15098","article_processing_charge":"Yes (via OA deal)","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","quality_controlled":"1","type":"journal_article","scopus_import":"1","publisher":"Springer Nature","author":[{"last_name":"Agresti","full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","orcid":"0000-0002-9573-2962"},{"first_name":"Eliseo","last_name":"Luongo","full_name":"Luongo, Eliseo"}],"publication":"Mathematische Annalen","year":"2024","department":[{"_id":"JuFi"}],"status":"public","publication_status":"epub_ahead","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00208-024-02812-0","open_access":"1"}],"oa_version":"Published Version","citation":{"ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024.","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0."},"date_created":"2024-03-10T23:00:54Z","title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.","lang":"eng"}],"doi":"10.1007/s00208-024-02812-0","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"oa":1,"article_type":"original"},{"publisher":"Society for Industrial and Applied Mathematics","author":[{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Lara","last_name":"Ost","full_name":"Ost, Lara"}],"type":"conference","quality_controlled":"1","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","article_processing_charge":"No","publication_identifier":{"eisbn":["9781611977912"]},"_id":"15093","editor":[{"full_name":"Woodruff, David P.","last_name":"Woodruff","first_name":"David P."}],"day":"04","date_updated":"2024-03-15T12:59:53Z","date_published":"2024-01-04T00:00:00Z","external_id":{"arxiv":["2311.01115"]},"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorigthms","start_date":"2024-01-07","end_date":"2024-01-10","location":"Alexandria, VA, USA"},"month":"01","page":"243 - 295","oa":1,"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right.","lang":"eng"}],"doi":"10.1137/1.9781611977912.11","date_created":"2024-03-08T10:27:39Z","title":"Dynamically maintaining the persistent homology of time series","citation":{"mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11."},"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"status":"for_moderation","id":"15094","relation":"dissertation_contains"}]},"main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"publication_status":"published","status":"public","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"year":"2024","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)"},{"external_id":{"arxiv":["2212.03128"]},"date_published":"2024-02-07T00:00:00Z","language":[{"iso":"eng"}],"month":"02","publication":"arXiv","publication_status":"submitted","day":"07","status":"public","department":[{"_id":"HeEd"}],"date_updated":"2024-03-15T12:59:53Z","year":"2024","date_created":"2024-03-08T10:13:59Z","title":"Chromatic alpha complexes","article_processing_charge":"No","citation":{"mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128."},"oa_version":"Preprint","article_number":"2212.03128","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"15091","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"related_material":{"record":[{"status":"for_moderation","id":"15094","relation":"dissertation_contains"}]},"oa":1,"author":[{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano"},{"first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","full_name":"Draganov, Ondrej","last_name":"Draganov"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"type":"preprint","abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"has_accepted_license":"1","volume":2608,"type":"book_chapter","scopus_import":"1","author":[{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Scheele","full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J."}],"publisher":"Springer Nature","_id":"12428","publication_identifier":{"eisbn":["9781071628874"],"isbn":["9781071628867"],"eissn":["1940-6029"]},"ddc":["570"],"pmid":1,"article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-02-03T10:58:56Z","series_title":"MIMB","day":"19","editor":[{"last_name":"Margadant","full_name":"Margadant, Coert","first_name":"Coert"}],"month":"01","language":[{"iso":"eng"}],"external_id":{"pmid":["36653709"]},"date_published":"2023-01-19T00:00:00Z","file_date_updated":"2023-02-03T10:56:39Z","doi":"10.1007/978-1-0716-2887-4_12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"file":[{"date_updated":"2023-02-03T10:56:39Z","success":1,"content_type":"application/pdf","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_id":"12500","access_level":"open_access","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","file_size":826598,"date_created":"2023-02-03T10:56:39Z","relation":"main_file"}],"oa":1,"page":"183-205","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"alternative_title":["Methods in Molecular Biology"],"citation":{"ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12"},"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","date_created":"2023-01-29T23:00:58Z","year":"2023","department":[{"_id":"EdHa"}],"status":"public","publication_status":"published","intvolume":" 2608","publication":"Cell Migration in Three Dimensions"},{"language":[{"iso":"eng"}],"date_published":"2023-01-20T00:00:00Z","month":"01","day":"20","date_updated":"2023-02-20T07:02:00Z","article_processing_charge":"No","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"_id":"12534","article_number":"013029","ddc":["530"],"publisher":"American Physical Society","author":[{"last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","first_name":"Areg","orcid":"0000-0001-9666-3543"},{"orcid":"0000-0001-6110-2359","first_name":"Alberto","full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"has_accepted_license":"1","volume":5,"type":"journal_article","scopus_import":"1","issue":"1","intvolume":" 5","publication":"Physical Review Research","department":[{"_id":"MiLe"}],"status":"public","publication_status":"published","year":"2023","citation":{"ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029.","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029"},"date_created":"2023-02-10T09:02:26Z","title":"Dissipative dynamics of an impurity with spin-orbit coupling","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","article_type":"original","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"doi":"10.1103/physrevresearch.5.013029","file_date_updated":"2023-02-13T10:38:10Z","file":[{"content_type":"application/pdf","date_updated":"2023-02-13T10:38:10Z","success":1,"file_size":865150,"date_created":"2023-02-13T10:38:10Z","relation":"main_file","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","access_level":"open_access","creator":"dernst","file_id":"12546","checksum":"6068b62874c0099628a108bb9c5c6bd2"}],"project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}]},{"keyword":["Genetics"],"department":[{"_id":"ScienComp"}],"status":"public","publication_status":"published","year":"2023","intvolume":" 55","publication":"Nature Genetics","article_type":"review","oa":1,"page":"333-345","file_date_updated":"2023-02-27T07:46:45Z","doi":"10.1038/s41588-022-01260-3","abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-02-27T07:46:45Z","success":1,"content_type":"application/pdf","file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","date_created":"2023-02-27T07:46:45Z","file_size":21484855,"relation":"main_file","file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","creator":"dernst"}],"citation":{"short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345."},"date_created":"2023-01-12T12:09:09Z","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","date_updated":"2023-02-27T07:48:24Z","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","month":"02","author":[{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559","first_name":"Jake"},{"last_name":"Viñas Gaza","full_name":"Viñas Gaza, Helena","first_name":"Helena"},{"last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj","first_name":"Vivek"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"publisher":"Springer Nature","has_accepted_license":"1","volume":55,"type":"journal_article","scopus_import":"1","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","article_processing_charge":"No","quality_controlled":"1","_id":"12158","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"ddc":["570","000"]},{"day":"01","date_updated":"2023-02-27T09:01:16Z","conference":{"location":"Florence, Italy","start_date":"2023-01-22","end_date":"2023-01-25","name":"SODA: Symposium on Discrete Algorithms"},"language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","month":"02","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","orcid":"0000-0002-1712-2165"},{"orcid":"0000-0001-5103-038X","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta"},{"first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","last_name":"Svoboda"}],"publisher":"Society for Industrial and Applied Mathematics","type":"conference","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","article_processing_charge":"No","quality_controlled":"1","_id":"12676","publication_identifier":{"isbn":["9781611977554"]},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"status":"public","publication_status":"published","year":"2023","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","oa":1,"page":"4590-4605","doi":"10.1137/1.9781611977554.ch173","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605."},"date_created":"2023-02-24T12:20:47Z","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"ec_funded":1,"oa_version":"Published Version"},{"year":"2023","date_updated":"2023-03-20T07:29:28Z","publication_status":"published","day":"25","status":"public","department":[{"_id":"DaAl"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","month":"02","date_published":"2023-02-25T00:00:00Z","external_id":{"arxiv":["2211.04986"]},"conference":{"location":"Montreal, QC, Canada","end_date":"2023-03-01","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"language":[{"iso":"eng"}],"scopus_import":"1","type":"conference","abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3572848.3577481","page":"107-118","publisher":"Association for Computing Machinery","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"oa":1,"oa_version":"Preprint","publication_identifier":{"isbn":["9798400700156"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"_id":"12735","quality_controlled":"1","date_created":"2023-03-19T23:00:58Z","title":"Fast and scalable channels in Kotlin Coroutines","article_processing_charge":"No","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118."}},{"page":"438-440","publisher":"Association for Computing Machinery","oa":1,"author":[{"full_name":"Aksenov, Vitaly","last_name":"Aksenov","first_name":"Vitaly"},{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"full_name":"Kokorin, Ilya","last_name":"Kokorin","first_name":"Ilya"}],"type":"conference_poster","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.","lang":"eng"}],"doi":"10.1145/3572848.3577512","quality_controlled":"1","date_created":"2023-03-19T23:00:58Z","title":"Unexpected scaling in path copying trees","article_processing_charge":"No","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","citation":{"ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"oa_version":"Published Version","publication_identifier":{"isbn":["9798400700156"]},"_id":"12736","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"publication_status":"published","day":"25","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"status":"public","year":"2023","date_updated":"2023-03-20T07:57:27Z","date_published":"2023-02-25T00:00:00Z","language":[{"iso":"eng"}],"conference":{"start_date":"2023-02-25","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"Montreal, QB, Canada"},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","month":"02"},{"publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"_id":"12760","article_number":"36","ddc":["000"],"acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","article_processing_charge":"No","quality_controlled":"1","volume":254,"has_accepted_license":"1","type":"conference","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"first_name":"Stefan","full_name":"Neumann, Stefan","last_name":"Neumann"},{"first_name":"Harald","full_name":"Räcke, Harald","last_name":"Räcke"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"month":"03","conference":{"location":"Hamburg, Germany","name":"STACS: Symposium on Theoretical Aspects of Computer Science","start_date":"2023-03-07","end_date":"2023-03-09"},"language":[{"iso":"eng"}],"date_published":"2023-03-01T00:00:00Z","external_id":{"arxiv":["2301.01744"]},"date_updated":"2023-03-27T06:46:27Z","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["LIPIcs"],"citation":{"mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36."},"date_created":"2023-03-26T22:01:07Z","title":"Dynamic maintenance of monotone dynamic programs and applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack."}],"file_date_updated":"2023-03-27T06:37:22Z","doi":"10.4230/LIPIcs.STACS.2023.36","file":[{"file_id":"12769","checksum":"22141ab8bc55188e2dfff665e5daecbd","date_created":"2023-03-27T06:37:22Z","file_size":872706,"relation":"main_file","file_name":"2023_LIPICS_HenzingerM.pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-03-27T06:37:22Z","success":1,"content_type":"application/pdf"}],"oa":1,"intvolume":" 254","publication":"40th International Symposium on Theoretical Aspects of Computer Science","year":"2023","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published"},{"oa_version":"Published Version","ec_funded":1,"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","date_created":"2023-03-08T15:19:45Z","citation":{"apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716"},"alternative_title":["ISTA Thesis"],"project":[{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"file":[{"relation":"source_file","date_created":"2023-03-08T15:08:46Z","file_size":23029260,"creator":"lburnett","access_level":"closed","file_name":"Burnett_Thesis_2023.docx","file_id":"12717","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-03-08T15:08:46Z"},{"content_type":"application/pdf","date_updated":"2023-03-08T15:08:46Z","success":1,"file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","creator":"lburnett","file_size":11959869,"date_created":"2023-03-08T15:08:46Z","relation":"main_file","checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"file_date_updated":"2023-03-08T15:08:46Z","doi":"10.15479/at:ista:12716","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"page":"178","oa":1,"year":"2023","publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"ddc":["599","573"],"_id":"12716","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"article_processing_charge":"No","type":"dissertation","has_accepted_license":"1","author":[{"first_name":"Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett","full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","month":"03","date_published":"2023-03-10T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-04-05T10:59:04Z","day":"10"},{"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"file":[{"date_updated":"2023-04-25T06:58:36Z","success":1,"content_type":"application/pdf","file_id":"12864","checksum":"120d2c2a38384058ad0630fdf8288312","file_size":16096413,"date_created":"2023-04-25T06:58:36Z","relation":"main_file","access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","creator":"dernst"}],"file_date_updated":"2023-04-25T06:58:36Z","doi":"10.1007/978-3-031-30820-8_32","abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"535-540","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"title":"Bubaak: Runtime monitoring of program verifiers","date_created":"2023-04-20T08:22:53Z","alternative_title":["LNCS"],"citation":{"chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540."},"year":"2023","publication_status":"published","status":"public","department":[{"_id":"ToHe"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","intvolume":" 13994","type":"conference","volume":13994,"has_accepted_license":"1","author":[{"first_name":"Marek","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"publisher":"Springer Nature","ddc":["000"],"_id":"12854","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031308208"],"isbn":["9783031308192"],"issn":["0302-9743"]},"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","date_updated":"2023-04-25T07:02:43Z","day":"20","month":"04","date_published":"2023-04-20T00:00:00Z","conference":{"location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22","end_date":"2023-04-27"},"language":[{"iso":"eng"}]},{"citation":{"chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","short":"A. Chern, S. Ishida, ArXiv (n.d.)."},"acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","article_processing_charge":"No","title":"Area formula for spherical polygons via prequantization","date_created":"2023-04-18T19:16:06Z","_id":"12846","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"oa_version":"Preprint","article_number":"2303.14555","oa":1,"author":[{"full_name":"Chern, Albert","last_name":"Chern","first_name":"Albert"},{"first_name":"Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"}],"doi":"10.48550/arXiv.2303.14555","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"type":"preprint","language":[{"iso":"eng"}],"external_id":{"arxiv":["2303.14555"]},"date_published":"2023-03-25T00:00:00Z","month":"03","publication":"arXiv","status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"submitted","day":"25","date_updated":"2023-04-25T06:51:21Z","year":"2023"},{"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12407"}]},"ec_funded":1,"title":"Vamos: Middleware for best-effort third-party monitoring","date_created":"2023-04-20T08:29:42Z","alternative_title":["LNCS"],"citation":{"short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"file":[{"success":1,"date_updated":"2023-04-25T07:16:36Z","content_type":"application/pdf","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_id":"12865","creator":"dernst","file_name":"2023_LNCS_ChalupaM.pdf","access_level":"open_access","relation":"main_file","file_size":580828,"date_created":"2023-04-25T07:16:36Z"}],"doi":"10.1007/978-3-031-30826-0_15","file_date_updated":"2023-04-25T07:16:36Z","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"260-281","oa":1,"publication":"Fundamental Approaches to Software Engineering","intvolume":" 13991","year":"2023","publication_status":"published","status":"public","department":[{"_id":"ToHe"}],"ddc":["000"],"_id":"12856","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031308260"],"isbn":["9783031308253"],"issn":["0302-9743"]},"quality_controlled":"1","article_processing_charge":"No","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","type":"conference","volume":13991,"has_accepted_license":"1","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"last_name":"Mühlböck","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","orcid":"0000-0003-1548-0177"},{"first_name":"Stefanie","last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"publisher":"Springer Nature","month":"04","date_published":"2023-04-20T00:00:00Z","language":[{"iso":"eng"}],"conference":{"name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"date_updated":"2023-04-25T07:19:07Z","day":"20"},{"keyword":["runtime monitoring","best effort","third party"],"department":[{"_id":"ToHe"}],"status":"public","publication_status":"published","year":"2023","alternative_title":["IST Austria Technical Report"],"citation":{"ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023."},"date_created":"2023-01-27T03:18:08Z","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","related_material":{"record":[{"relation":"later_version","id":"12856","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"page":"38","doi":"10.15479/AT:ISTA:12407","file_date_updated":"2023-01-27T03:18:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-01-27T03:18:34Z","creator":"fmuehlbo","access_level":"open_access","file_name":"main.pdf","relation":"main_file","date_created":"2023-01-27T03:18:34Z","file_size":662409,"checksum":"55426e463fdeafe9777fc3ff635154c7","file_id":"12408"}],"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"language":[{"iso":"eng"}],"date_published":"2023-01-27T00:00:00Z","month":"01","day":"27","date_updated":"2023-04-25T07:19:06Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","article_processing_charge":"No","_id":"12407","publication_identifier":{"eissn":["2664-1690"]},"ddc":["005"],"author":[{"last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek","first_name":"Marek"},{"orcid":"0000-0003-1548-0177","first_name":"Fabian","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck"},{"last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","type":"technical_report"},{"citation":{"ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2."},"date_created":"2023-02-23T09:13:49Z","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"oa_version":"Published Version","article_type":"original","oa":1,"doi":"10.1186/s13059-022-02844-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}],"intvolume":" 24","publication":"Genome Biology","department":[{"_id":"XiFe"}],"status":"public","publication_status":"published","year":"2023","pmid":1,"article_processing_charge":"No","quality_controlled":"1","_id":"12668","publication_identifier":{"issn":["1474-760X"]},"article_number":"7","author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"first_name":"Yiman","full_name":"Yang, Yiman","last_name":"Yang"},{"last_name":"Chen","full_name":"Chen, Jinchao","first_name":"Jinchao"},{"full_name":"Lin, Xuelei","last_name":"Lin","first_name":"Xuelei"},{"first_name":"Hao","full_name":"Zhang, Hao","last_name":"Zhang"},{"last_name":"Wang","full_name":"Wang, Hao","first_name":"Hao"},{"first_name":"Hongzhe","last_name":"Wang","full_name":"Wang, Hongzhe"},{"full_name":"Bie, Xiaomin","last_name":"Bie","first_name":"Xiaomin"},{"last_name":"Jiang","full_name":"Jiang, Jiafu","first_name":"Jiafu"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"full_name":"Fu, Xiangdong","last_name":"Fu","first_name":"Xiangdong"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"full_name":"Xiao, Jun","last_name":"Xiao","first_name":"Jun"}],"publisher":"Springer Nature","volume":24,"type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["36639687"]},"date_published":"2023-01-13T00:00:00Z","month":"01","day":"13","extern":"1","date_updated":"2023-05-08T10:52:49Z"},{"main_file_link":[{"url":"https://doi.org/10.1002/chem.202202967","open_access":"1"}],"oa_version":"Published Version","citation":{"ieee":"M. Traxler et al., “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European Journal, vol. 29, no. 4. Wiley, 2023.","apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202202967","chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley, 2023. https://doi.org/10.1002/chem.202202967.","ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967.","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).","mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967.","ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 2023;29(4). doi:10.1002/chem.202202967"},"title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","date_created":"2023-05-08T08:25:34Z","doi":"10.1002/chem.202202967","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation.","lang":"eng"}],"oa":1,"article_type":"original","intvolume":" 29","publication":"Chemistry – A European Journal","issue":"4","year":"2023","keyword":["General Chemistry","Catalysis","Organic Chemistry"],"status":"public","publication_status":"published","_id":"12920","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"article_number":"e202202967","article_processing_charge":"No","quality_controlled":"1","volume":29,"scopus_import":"1","type":"journal_article","author":[{"last_name":"Traxler","full_name":"Traxler, Michael","first_name":"Michael"},{"last_name":"Reischauer","full_name":"Reischauer, Susanne","first_name":"Susanne"},{"last_name":"Vogl","full_name":"Vogl, Sarah","first_name":"Sarah"},{"first_name":"Jérôme","full_name":"Roeser, Jérôme","last_name":"Roeser"},{"last_name":"Rabeah","full_name":"Rabeah, Jabor","first_name":"Jabor"},{"full_name":"Penschke, Christopher","last_name":"Penschke","first_name":"Christopher"},{"first_name":"Peter","last_name":"Saalfrank","full_name":"Saalfrank, Peter"},{"last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X"},{"first_name":"Arne","last_name":"Thomas","full_name":"Thomas, Arne"}],"publisher":"Wiley","month":"01","language":[{"iso":"eng"}],"date_published":"2023-01-18T00:00:00Z","extern":"1","date_updated":"2023-05-15T08:39:24Z","day":"18"},{"date_published":"2023-04-06T00:00:00Z","language":[{"iso":"eng"}],"month":"04","day":"06","date_updated":"2023-05-15T08:35:48Z","extern":"1","quality_controlled":"1","article_processing_charge":"No","article_number":"e202201583","publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"_id":"12921","publisher":"Wiley","author":[{"first_name":"Amiera","full_name":"Madani, Amiera","last_name":"Madani"},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus"}],"scopus_import":"1","type":"journal_article","volume":15,"issue":"7","publication":"ChemCatChem","intvolume":" 15","publication_status":"published","status":"public","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Catalysis"],"year":"2023","title":"In situ reaction monitoring in photocatalytic organic synthesis","date_created":"2023-05-08T08:25:55Z","citation":{"ama":"Madani A, Pieber B. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 2023;15(7). doi:10.1002/cctc.202201583","mla":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem, vol. 15, no. 7, e202201583, Wiley, 2023, doi:10.1002/cctc.202201583.","short":"A. Madani, B. Pieber, ChemCatChem 15 (2023).","chicago":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202201583.","ista":"Madani A, Pieber B. 2023. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 15(7), e202201583.","apa":"Madani, A., & Pieber, B. (2023). In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202201583","ieee":"A. Madani and B. Pieber, “In situ reaction monitoring in photocatalytic organic synthesis,” ChemCatChem, vol. 15, no. 7. Wiley, 2023."},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1002/cctc.202201583","open_access":"1"}],"article_type":"original","oa":1,"abstract":[{"lang":"eng","text":"Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/cctc.202201583"},{"publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"status":"public","oa_version":"Preprint","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.04014"}],"title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","date_created":"2023-05-22T08:02:02Z","citation":{"apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113"},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis."}],"doi":"10.1145/3564246.3585113","page":"1768-1776","oa":1,"month":"06","date_published":"2023-06-02T00:00:00Z","external_id":{"arxiv":["2303.04014"]},"conference":{"location":"Orlando, FL, United States","name":"STOC: Symposium on Theory of Computing","end_date":"2023-06-23","start_date":"2023-06-20"},"language":[{"iso":"eng"}],"date_updated":"2023-05-22T08:15:19Z","day":"02","publication_identifier":{"isbn":["9781450399135"]},"_id":"13048","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","type":"conference","publisher":"Association for Computing Machinery","author":[{"first_name":"André","full_name":"Lieutier, André","last_name":"Lieutier"},{"first_name":"Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}]},{"oa":1,"author":[{"first_name":"Elena-Alexandra","last_name":"Peste","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vladu, Adrian","last_name":"Vladu","first_name":"Adrian"},{"first_name":"Eldar","last_name":"Kurtic","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"type":"conference","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"CrAM: A Compression-Aware Minimizer","date_created":"2023-05-23T11:36:18Z","quality_controlled":"1","citation":{"apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations ."},"article_processing_charge":"No","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","oa_version":"Preprint","_id":"13053","related_material":{"record":[{"id":"13074","status":"public","relation":"dissertation_contains"}]},"main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"ec_funded":1,"publication_status":"accepted","status":"public","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"date_updated":"2023-06-01T12:54:45Z","year":"2023","external_id":{"arxiv":["2207.14200"]},"date_published":"2023-05-01T00:00:00Z","conference":{"location":"Kigali, Rwanda ","end_date":"2023-05-05","start_date":"2023-05-01","name":"ICLR: International Conference on Learning Representations"},"language":[{"iso":"eng"}],"month":"05","publication":"11th International Conference on Learning Representations "},{"intvolume":" 13940","publication":"Public-Key Cryptography - PKC 2023","status":"public","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2023","citation":{"ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553."},"alternative_title":["LNCS"],"title":"Certifying giant nonprimes","date_created":"2023-06-18T22:00:47Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/238"}],"oa_version":"Submitted Version","oa":1,"page":"530-553","abstract":[{"text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-31368-4_19","language":[{"iso":"eng"}],"conference":{"location":"Atlanta, GA, United States","name":"PKC: Public-Key Cryptography","start_date":"2023-05-07","end_date":"2023-05-10"},"date_published":"2023-05-02T00:00:00Z","month":"05","day":"02","date_updated":"2023-06-19T08:03:37Z","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031313677"],"issn":["0302-9743"]},"_id":"13143","publisher":"Springer Nature","author":[{"full_name":"Hoffmann, Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","first_name":"Charlotte"},{"last_name":"Hubáček","full_name":"Hubáček, Pavel","first_name":"Pavel"},{"first_name":"Chethan","last_name":"Kamath","full_name":"Kamath, Chethan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"}],"volume":13940,"scopus_import":"1","type":"conference"},{"has_accepted_license":"1","volume":13993,"type":"conference","scopus_import":"1","publisher":"Springer Nature","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","first_name":"Dorde"}],"publication_identifier":{"isbn":["9783031308222"],"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"13142","ddc":["000"],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-06-19T08:30:54Z","day":"22","month":"04","language":[{"iso":"eng"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"date_published":"2023-04-22T00:00:00Z","abstract":[{"text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-30823-9_1","file_date_updated":"2023-06-19T08:29:30Z","file":[{"file_id":"13150","checksum":"3d8a8bb24d211bc83360dfc2fd744307","date_created":"2023-06-19T08:29:30Z","file_size":528455,"relation":"main_file","file_name":"2023_LNCS_Chatterjee.pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-06-19T08:29:30Z","success":1,"content_type":"application/pdf"}],"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"page":"3-25","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["LNCS"],"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1."},"title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","date_created":"2023-06-18T22:00:47Z","year":"2023","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"status":"public","publication_status":"published","intvolume":" 13993","publication":"Tools and Algorithms for the Construction and Analysis of Systems "},{"quality_controlled":"1","article_processing_charge":"No","ddc":["000"],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"_id":"13141","publisher":"Springer Nature","author":[{"first_name":"Ashwani","full_name":"Anand, Ashwani","last_name":"Anand"},{"orcid":"0000-0001-9864-7475","first_name":"Kaushik","full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik"},{"first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash","last_name":"Nayak"},{"full_name":"Schmuck, Anne Kathrin","last_name":"Schmuck","first_name":"Anne Kathrin"}],"type":"conference","scopus_import":"1","volume":13994,"has_accepted_license":"1","date_published":"2023-04-20T00:00:00Z","language":[{"iso":"eng"}],"conference":{"end_date":"2023-04-27","start_date":"2023-04-22","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Paris, France"},"month":"04","day":"20","date_updated":"2023-06-19T08:49:46Z","title":"Computing adequately permissive assumptions for synthesis","date_created":"2023-06-18T22:00:47Z","citation":{"apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15"},"alternative_title":["LNCS"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","page":"211-228","oa":1,"file":[{"creator":"dernst","file_name":"2023_LNCS_Anand.pdf","access_level":"open_access","relation":"main_file","file_size":521425,"date_created":"2023-06-19T08:43:21Z","checksum":"60dcafc1b4f6f070be43bad3fe877974","file_id":"13151","content_type":"application/pdf","success":1,"date_updated":"2023-06-19T08:43:21Z"}],"abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-30820-8_15","file_date_updated":"2023-06-19T08:43:21Z","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","intvolume":" 13994","publication_status":"published","department":[{"_id":"ToHe"}],"status":"public","year":"2023"},{"type":"dissertation","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","first_name":"Victoria"}],"ddc":["570","571"],"publication_identifier":{"issn":["2663 - 337X"]},"_id":"12826","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"article_processing_charge":"No","date_updated":"2023-06-23T09:47:36Z","day":"18","month":"04","date_published":"2023-04-18T00:00:00Z","language":[{"iso":"eng"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"file":[{"date_updated":"2023-04-20T09:26:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","creator":"vpokusae","file_name":"Thesis_Pokusaeva.docx","access_level":"closed","relation":"source_file","date_created":"2023-04-20T09:14:38Z","file_size":14507243},{"creator":"vpokusae","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","relation":"main_file","file_size":10090711,"date_created":"2023-04-20T09:14:44Z","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","file_id":"12858","content_type":"application/pdf","success":1,"date_updated":"2023-04-20T09:14:44Z"}],"abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/at:ista:12826","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2023-04-20T09:26:51Z","page":"106","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"date_created":"2023-04-14T14:56:04Z","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","citation":{"ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826"},"alternative_title":["ISTA Thesis"],"year":"2023","publication_status":"published","status":"public","department":[{"_id":"MaJö"},{"_id":"GradSch"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"date_created":"2022-09-11T22:01:57Z","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","citation":{"mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."},"file":[{"creator":"dernst","file_name":"2023_Algorithmica_Edelsbrunner.pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-20T10:02:48Z","file_size":911017,"checksum":"71685ca5121f4c837f40c3f8eb50c915","file_id":"12322","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T10:02:48Z"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"file_date_updated":"2023-01-20T10:02:48Z","doi":"10.1007/s00453-022-01027-6","page":"277-295","article_type":"original","oa":1,"publication":"Algorithmica","intvolume":" 85","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"status":"public","ddc":["510"],"publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"_id":"12086","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":85,"publisher":"Springer Nature","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F"}],"month":"01","isi":1,"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000846967100001"]},"language":[{"iso":"eng"}],"date_updated":"2023-06-27T12:53:43Z","day":"01"},{"doi":"10.1007/s00028-022-00859-7","file_date_updated":"2023-01-20T10:45:06Z","abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"},{"name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"file":[{"success":1,"date_updated":"2023-01-20T10:45:06Z","content_type":"application/pdf","file_id":"12325","checksum":"1f34f3e2cb521033de6154f274ea3a4e","relation":"main_file","file_size":422612,"date_created":"2023-01-20T10:45:06Z","creator":"dernst","access_level":"open_access","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf"}],"oa":1,"article_type":"original","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023."},"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","date_created":"2023-01-08T23:00:53Z","year":"2023","department":[{"_id":"JaMa"}],"status":"public","publication_status":"published","intvolume":" 23","publication":"Journal of Evolution Equations","issue":"1","volume":23,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","first_name":"Lorenzo"},{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior"}],"publisher":"Springer Nature","_id":"12104","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"article_number":"9","ddc":["510"],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","quality_controlled":"1","date_updated":"2023-06-28T11:54:35Z","day":"01","isi":1,"month":"01","language":[{"iso":"eng"}],"external_id":{"isi":["000906214600004"]},"date_published":"2023-01-01T00:00:00Z"},{"title":"Quantitative safety and liveness","date_created":"2023-01-31T07:23:56Z","alternative_title":["LNCS"],"citation":{"chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"page":"349-370","oa":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"file":[{"success":1,"date_updated":"2023-01-31T07:22:21Z","content_type":"application/pdf","file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e","relation":"main_file","date_created":"2023-01-31T07:22:21Z","file_size":449027,"creator":"esarac","file_name":"qsl.pdf","access_level":"open_access"},{"content_type":"application/pdf","success":1,"date_updated":"2023-06-19T10:28:09Z","creator":"dernst","file_name":"2023_LNCS_HenzingerT.pdf","access_level":"open_access","relation":"main_file","file_size":1048171,"date_created":"2023-06-19T10:28:09Z","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153"}],"doi":"10.1007/978-3-031-30829-1_17","file_date_updated":"2023-06-19T10:28:09Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"publication":"26th International Conference Foundations of Software Science and Computation Structures","intvolume":" 13992","publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"year":"2023","quality_controlled":"1","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","article_processing_charge":"No","ddc":["000"],"_id":"12467","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031308284"]},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E"}],"publisher":"Springer Nature","type":"conference","scopus_import":"1","volume":13992,"has_accepted_license":"1","external_id":{"arxiv":["2301.11175"]},"date_published":"2023-04-21T00:00:00Z","conference":{"start_date":"2023-04-22","end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures","location":"Paris, France"},"language":[{"iso":"eng"}],"month":"04","day":"21","date_updated":"2023-07-14T11:20:27Z"},{"ddc":["000"],"article_number":"116","_id":"13179","publication_identifier":{"eissn":["2475-1421"]},"quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":7,"author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry","first_name":"Dmitry"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"publisher":"Association for Computing Machinery ","month":"06","date_published":"2023-06-06T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-07-17T08:43:19Z","day":"06","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"title":"CQS: A formally-verified framework for fair and abortable synchronization","date_created":"2023-07-02T22:00:43Z","citation":{"mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230."},"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-07-03T13:09:39Z","relation":"main_file","date_created":"2023-07-03T13:09:39Z","file_size":1266773,"creator":"alisjak","file_name":"2023_ACMProgram.Lang._Koval.pdf","access_level":"open_access","file_id":"13187","checksum":"5dba6e73f0ed79adbdae14d165bc2f68"}],"file_date_updated":"2023-07-03T13:09:39Z","doi":"10.1145/3591230","abstract":[{"text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"publication":"Proceedings of the ACM on Programming Languages","intvolume":" 7","year":"2023","publication_status":"published","department":[{"_id":"DaAl"}],"status":"public"},{"month":"05","external_id":{"arxiv":["2203.06881"]},"date_published":"2023-05-26T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-07-17T08:39:19Z","day":"26","_id":"13180","publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"quality_controlled":"1","article_processing_charge":"No","type":"journal_article","scopus_import":"1","volume":16,"author":[{"first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"id":"3572849A-F248-11E8-B48F-1D18A9856A87","full_name":"Lyczak, Julian","last_name":"Lyczak","first_name":"Julian"},{"full_name":"Sarapin, Roman","last_name":"Sarapin","first_name":"Roman"}],"publisher":"Mathematical Sciences Publishers","publication":"Involve","intvolume":" 16","issue":"2","year":"2023","publication_status":"published","status":"public","department":[{"_id":"TiBr"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.06881"}],"date_created":"2023-07-02T22:00:43Z","title":"Local solubility for a family of quadrics over a split quadric surface","citation":{"ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331.","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331"},"doi":"10.2140/involve.2023.16.331","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface","lang":"eng"}],"page":"331-342","article_type":"original","oa":1},{"intvolume":" 13904","publication":"International Conference on Integer Programming and Combinatorial Optimization","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published","year":"2023","alternative_title":["LNCS"],"citation":{"short":"D.W. Zheng, M.H. Henzinger, in:, International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” International Conference on Integer Programming and Combinatorial Optimization, vol. 13904, Springer Nature, 2023, pp. 453–65, doi:10.1007/978-3-031-32726-1_32.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. In: International Conference on Integer Programming and Combinatorial Optimization. Vol 13904. Springer Nature; 2023:453-465. doi:10.1007/978-3-031-32726-1_32","apa":"Zheng, D. W., & Henzinger, M. H. (2023). Multiplicative auction algorithm for approximate maximum weight bipartite matching. In International Conference on Integer Programming and Combinatorial Optimization (Vol. 13904, pp. 453–465). Madison, WI, United States: Springer Nature. https://doi.org/10.1007/978-3-031-32726-1_32","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” in International Conference on Integer Programming and Combinatorial Optimization, Madison, WI, United States, 2023, vol. 13904, pp. 453–465.","ista":"Zheng DW, Henzinger MH. 2023. Multiplicative auction algorithm for approximate maximum weight bipartite matching. International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 13904, 453–465.","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” In International Conference on Integer Programming and Combinatorial Optimization, 13904:453–65. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32726-1_32."},"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","date_created":"2023-07-16T22:01:11Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"ec_funded":1,"oa_version":"Preprint","oa":1,"page":"453-465","doi":"10.1007/978-3-031-32726-1_32","abstract":[{"text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"language":[{"iso":"eng"}],"conference":{"location":"Madison, WI, United States","start_date":"2023-06-21","end_date":"2023-06-23","name":"IPCO: Integer Programming and Combinatorial Optimization"},"external_id":{"arxiv":["2301.09217"]},"date_published":"2023-05-22T00:00:00Z","month":"05","day":"22","date_updated":"2023-07-18T07:08:51Z","article_processing_charge":"No","acknowledgement":"The first author thanks to Chandra Chekuri for useful discussions about this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","quality_controlled":"1","_id":"13236","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031327254"]},"author":[{"full_name":"Zheng, Da Wei","last_name":"Zheng","first_name":"Da Wei"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"publisher":"Springer Nature","volume":13904,"type":"conference","scopus_import":"1"},{"publication_status":"accepted","day":"01","status":"public","department":[{"_id":"ScienComp"}],"date_updated":"2023-07-18T09:32:16Z","year":"2023","date_published":"2023-07-01T00:00:00Z","conference":{"location":"Maribor, Slovenia","end_date":"2023-06-15","start_date":"2023-06-12","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"language":[{"iso":"eng"}],"month":"07","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","page":"42-42","oa":1,"author":[{"last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","first_name":"Stephan"},{"first_name":"Michael F","last_name":"Alexander","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Alexander, Michael F"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"}],"publisher":"EuroCC","file":[{"success":1,"date_updated":"2023-07-18T09:28:30Z","content_type":"application/pdf","checksum":"0ab6173cd5c5634ed773cd37ff012681","file_id":"13250","creator":"dernst","file_name":"2023_ASHPC_Elefante.pdf","access_level":"open_access","relation":"main_file","file_size":380354,"date_created":"2023-07-18T09:28:30Z"}],"type":"conference_abstract","file_date_updated":"2023-07-18T09:28:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","date_created":"2023-06-23T11:03:18Z","title":"Cryo-EM software packages: A sys-admins point of view","quality_controlled":"1","citation":{"mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42."},"article_processing_charge":"No","ddc":["000"],"oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"13162"},{"date_created":"2023-06-23T11:01:23Z","title":"Running Windows-applications on a Linux HPC cluster using WINE","citation":{"chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59."},"oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"page":"59-59","oa":1,"file":[{"date_updated":"2023-07-18T09:18:55Z","success":1,"content_type":"application/pdf","checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_id":"13249","file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access","creator":"dernst","file_size":316959,"date_created":"2023-07-18T09:18:55Z","relation":"main_file"}],"file_date_updated":"2023-07-18T09:18:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","publication_status":"inpress","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","year":"2023","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","ddc":["000"],"_id":"13161","author":[{"orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"}],"publisher":"EuroCC","type":"conference_abstract","has_accepted_license":"1","date_published":"2023-07-01T00:00:00Z","language":[{"iso":"eng"}],"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2023-06-13","end_date":"2023-06-15","location":"Maribor, Slovenia"},"month":"07","day":"01","date_updated":"2023-07-18T09:30:54Z"},{"ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158"},"date_created":"2023-07-18T11:13:17Z","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"file_date_updated":"2023-07-19T06:55:39Z","doi":"10.1021/acs.jpclett.3c01158","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"file":[{"success":1,"date_updated":"2023-07-19T06:55:39Z","content_type":"application/pdf","checksum":"c0c040063f06a51b9c463adc504f1a23","file_id":"13253","creator":"dernst","access_level":"open_access","file_name":"2023_JourPhysChemistry_Wei.pdf","relation":"main_file","date_created":"2023-07-19T06:55:39Z","file_size":2121252}],"article_type":"original","oa":1,"page":"6309-6314","intvolume":" 14","publication":"The Journal of Physical Chemistry Letters","issue":"27","year":"2023","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"status":"public","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"publication_status":"published","publication_identifier":{"eissn":["1948-7185"]},"_id":"13251","ddc":["530"],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","quality_controlled":"1","has_accepted_license":"1","volume":14,"type":"journal_article","publisher":"American Chemical Society","author":[{"orcid":"0000-0001-8913-9719","first_name":"Yujing","id":"0c5ff007-2600-11ee-b896-98bd8d663294","full_name":"Wei, Yujing","last_name":"Wei"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"},{"first_name":"Dusan","full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc"},{"first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov"},{"last_name":"Bakr","full_name":"Bakr, Osman M.","first_name":"Osman M."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","orcid":"0000-0002-7183-5203"}],"isi":1,"month":"07","language":[{"iso":"eng"}],"date_published":"2023-07-05T00:00:00Z","external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"date_updated":"2023-07-19T06:59:19Z","day":"05"},{"date_updated":"2023-07-31T08:38:38Z","day":"05","month":"07","language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2023-07-14","start_date":"2023-07-10","location":"Paderborn, Germany"},"external_id":{"arxiv":["2305.03447"]},"date_published":"2023-07-05T00:00:00Z","has_accepted_license":"1","volume":261,"type":"conference","author":[{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kebis, Pavol","last_name":"Kebis","first_name":"Pavol"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","first_name":"Naci E"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"13292","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"ddc":["000"],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","article_processing_charge":"Yes","quality_controlled":"1","year":"2023","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"status":"public","publication_status":"published","intvolume":" 261","publication":"50th International Colloquium on Automata, Languages, and Programming","doi":"10.4230/LIPIcs.ICALP.2023.129","file_date_updated":"2023-07-24T15:11:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-07-24T15:11:05Z","relation":"main_file","file_size":859379,"date_created":"2023-07-24T15:11:05Z","creator":"esarac","access_level":"open_access","file_name":"icalp23.pdf","file_id":"13293","checksum":"5d4c8932ef3450615a53b9bb15d92eb2"}],"oa":1,"page":"129:1--129:20","ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"alternative_title":["LIPIcs"],"citation":{"ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129"},"date_created":"2023-07-24T15:11:41Z","title":"Regular methods for operator precedence languages"},{"external_id":{"arxiv":["2211.01923"]},"date_published":"2023-04-14T00:00:00Z","language":[{"iso":"eng"}],"month":"04","day":"14","date_updated":"2023-07-31T09:03:28Z","quality_controlled":"1","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","article_processing_charge":"No","ddc":["530"],"article_number":"029","_id":"13277","publication_identifier":{"issn":["2666-9366"]},"author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"first_name":"Stefano","orcid":"0000-0002-4842-6671","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","full_name":"De Nicola, Stefano"},{"last_name":"Wald","full_name":"Wald, Sascha","first_name":"Sascha"},{"first_name":"Andrea","last_name":"Gambassi","full_name":"Gambassi, Andrea"}],"publisher":"SciPost Foundation","type":"journal_article","volume":6,"has_accepted_license":"1","issue":"2","publication":"SciPost Physics Core","intvolume":" 6","publication_status":"published","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"status":"public","department":[{"_id":"MaSe"}],"year":"2023","date_created":"2023-07-24T10:47:46Z","title":"Stochastic representation of the quantum quartic oscillator","citation":{"ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029.","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"oa":1,"article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2023-07-31T09:02:27Z","success":1,"access_level":"open_access","file_name":"2023_SciPostPhysCore_Tucci.pdf","creator":"dernst","date_created":"2023-07-31T09:02:27Z","file_size":523236,"relation":"main_file","checksum":"b472bc82108747eda5d52adf9e2ac7f3","file_id":"13329"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.21468/scipostphyscore.6.2.029","file_date_updated":"2023-07-31T09:02:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}]},{"ec_funded":1,"related_material":{"record":[{"status":"public","id":"13275","relation":"research_data"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12."},"date_created":"2023-07-24T10:47:15Z","title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-07-31T09:09:23Z","doi":"10.21468/scipostphyscodeb.12","file":[{"success":1,"date_updated":"2023-07-31T09:09:23Z","content_type":"application/pdf","checksum":"f583a70fe915d2208c803f5afb426daa","file_id":"13330","creator":"dernst","access_level":"open_access","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","relation":"main_file","date_created":"2023-07-31T09:09:23Z","file_size":551418}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"article_type":"original","publication":"SciPost Physics Codebases","year":"2023","status":"public","department":[{"_id":"MiLe"}],"publication_status":"published","publication_identifier":{"issn":["2949-804X"]},"_id":"13276","ddc":["530"],"article_number":"12","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","article_processing_charge":"No","quality_controlled":"1","has_accepted_license":"1","type":"journal_article","publisher":"SciPost Foundation","author":[{"last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas","first_name":"Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"month":"04","language":[{"iso":"eng"}],"date_published":"2023-04-19T00:00:00Z","external_id":{"arxiv":["2202.04603"]},"date_updated":"2023-07-31T09:16:02Z","day":"19"},{"month":"04","date_published":"2023-04-19T00:00:00Z","year":"2023","date_updated":"2023-07-31T09:16:02Z","department":[{"_id":"MiLe"}],"status":"public","day":"19","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"_id":"13275","related_material":{"record":[{"status":"public","id":"13276","relation":"used_in_publication"}]},"ddc":["530"],"oa_version":"Published Version","citation":{"ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023."},"article_processing_charge":"No","title":"Codebase release 1.0 for FermiFCI","date_created":"2023-07-24T10:46:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"doi":"10.21468/scipostphyscodeb.12-r1.0","type":"research_data_reference","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"SciPost Foundation","author":[{"first_name":"Lukas","full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller"},{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"oa":1},{"file":[{"file_id":"13334","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","relation":"main_file","date_created":"2023-07-31T10:53:08Z","file_size":2087937,"creator":"dernst","access_level":"open_access","file_name":"2023_SPAA_Fedorov.pdf","success":1,"date_updated":"2023-07-31T10:53:08Z","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"file_date_updated":"2023-07-31T10:53:08Z","doi":"10.1145/3558481.3591082","page":"261-271","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","date_created":"2023-07-23T22:01:12Z","title":"Provably-efficient and internally-deterministic parallel Union-Find","citation":{"short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271."},"year":"2023","publication_status":"published","status":"public","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","scopus_import":"1","type":"conference","has_accepted_license":"1","publisher":"Association for Computing Machinery","author":[{"last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander","first_name":"Alexander"},{"last_name":"Hashemi","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba","first_name":"Diba"},{"first_name":"Giorgi","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"ddc":["000"],"publication_identifier":{"isbn":["9781450395458"]},"_id":"13262","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","date_updated":"2023-07-31T10:54:32Z","day":"17","month":"06","date_published":"2023-06-17T00:00:00Z","external_id":{"arxiv":["2304.09331"]},"conference":{"location":"Orlando, FL, United States","start_date":"2023-06-17","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"language":[{"iso":"eng"}]},{"isi":1,"month":"02","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","external_id":{"isi":["000815663700001"]},"date_updated":"2023-08-01T12:25:44Z","day":"01","publication_identifier":{"eissn":["1752-4571"]},"_id":"11479","ddc":["576"],"article_processing_charge":"No","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","quality_controlled":"1","volume":16,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Wiley","author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"intvolume":" 16","publication":"Evolutionary Applications","issue":"2","year":"2023","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"status":"public","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023."},"date_created":"2022-07-03T22:01:33Z","title":"Ten years of demographic modelling of divergence and speciation in the sea","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"file_date_updated":"2023-02-27T07:10:17Z","doi":"10.1111/eva.13428","file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-02-27T07:10:17Z","relation":"main_file","date_created":"2023-02-27T07:10:17Z","file_size":2269822,"creator":"dernst","file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access","file_id":"12685","checksum":"d4d6fa9ddf36643af994a6a757919afb"}],"article_type":"original","oa":1,"page":"542-559"},{"article_type":"original","oa":1,"doi":"10.1038/s41598-022-19827-9","file_date_updated":"2023-01-23T07:53:23Z","abstract":[{"text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"a8b83739f4a951e83e0b2a778f03b327","file_id":"12336","access_level":"open_access","file_name":"2023_ScientificReports_Gomez.pdf","creator":"dernst","file_size":2167792,"date_created":"2023-01-23T07:53:23Z","relation":"main_file","date_updated":"2023-01-23T07:53:23Z","success":1,"content_type":"application/pdf"}],"citation":{"chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9."},"date_created":"2023-01-22T23:00:55Z","title":"New approaches to epidemic modeling on networks","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2023","intvolume":" 13","publication":"Scientific Reports","author":[{"last_name":"Gómez","full_name":"Gómez, Arturo","first_name":"Arturo"},{"first_name":"Goncalo","last_name":"Oliveira","id":"58abbde8-f455-11eb-a497-98c8fd71b905","full_name":"Oliveira, Goncalo"}],"publisher":"Springer Nature","volume":13,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","article_processing_charge":"No","quality_controlled":"1","_id":"12329","publication_identifier":{"eissn":["2045-2322"]},"ddc":["510"],"article_number":"468","day":"10","date_updated":"2023-08-01T12:31:40Z","language":[{"iso":"eng"}],"external_id":{"isi":["001003345000051"]},"date_published":"2023-01-10T00:00:00Z","isi":1,"month":"01"},{"date_updated":"2023-08-01T12:23:55Z","day":"01","isi":1,"month":"04","language":[{"iso":"eng"}],"external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"date_published":"2023-04-01T00:00:00Z","volume":2023,"type":"journal_article","author":[{"orcid":"0000-0001-7302-8256","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch"}],"publisher":"Oxford Academic","_id":"9034","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"article_processing_charge":"No","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","quality_controlled":"1","year":"2023","department":[{"_id":"TiBr"}],"status":"public","publication_status":"published","intvolume":" 2023","publication":"International Mathematics Research Notices","issue":"8","doi":"10.1093/imrn/rnac048","abstract":[{"text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"article_type":"original","page":"6780-6808","main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"oa_version":"Preprint","citation":{"ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023."},"title":"Integral points of bounded height on a log Fano threefold","date_created":"2021-01-22T09:31:09Z"},{"day":"16","date_updated":"2023-08-01T12:39:58Z","language":[{"iso":"eng"}],"external_id":{"pmid":["PPR559293 "],"isi":["000961542100001"]},"date_published":"2023-03-16T00:00:00Z","isi":1,"month":"03","author":[{"first_name":"Lumi","full_name":"Viljakainen, Lumi","last_name":"Viljakainen"},{"last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","first_name":"Matthias","orcid":"0000-0002-3712-925X"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana","first_name":"Jaana"},{"orcid":"0000-0001-7425-2372","first_name":"Jinook","full_name":"Oh, Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","last_name":"Oh"},{"last_name":"Tolonen","full_name":"Tolonen, Lassi","first_name":"Lassi"},{"last_name":"Eder","full_name":"Eder, Thomas","first_name":"Thomas"},{"full_name":"Rattei, Thomas","last_name":"Rattei","first_name":"Thomas"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"publisher":"Frontiers","volume":14,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","pmid":1,"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","quality_controlled":"1","_id":"12469","publication_identifier":{"eissn":["1664-302X"]},"article_number":"1119002","ddc":["570"],"department":[{"_id":"SyCr"}],"status":"public","publication_status":"published","year":"2023","intvolume":" 14","publication":"Frontiers in Microbiology","oa":1,"article_type":"original","doi":"10.3389/fmicb.2023.1119002","file_date_updated":"2023-04-17T07:49:09Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management."}],"project":[{"_id":"25DF61D8-B435-11E9-9278-68D0E5697425","name":"Viral pathogens and social immunity in ants","grant_number":"M02076","call_identifier":"FWF"}],"file":[{"content_type":"application/pdf","date_updated":"2023-04-17T07:49:09Z","success":1,"file_size":4866332,"date_created":"2023-04-17T07:49:09Z","relation":"main_file","access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","creator":"dernst","file_id":"12843","checksum":"cd52292963acce1111634d9fac08c699"}],"citation":{"ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023."},"date_created":"2023-01-31T08:13:40Z","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7."},"title":"Local criteria for triangulating general manifolds","date_created":"2023-01-16T10:04:06Z","doi":"10.1007/s00454-022-00431-7","file_date_updated":"2023-02-02T11:01:10Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-02-02T11:01:10Z","creator":"dernst","access_level":"open_access","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","relation":"main_file","file_size":582850,"date_created":"2023-02-02T11:01:10Z","checksum":"46352e0ee71e460848f88685ca852681","file_id":"12488"}],"oa":1,"article_type":"original","page":"156-191","intvolume":" 69","publication":"Discrete & Computational Geometry","year":"2023","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"status":"public","department":[{"_id":"HeEd"}],"publication_status":"published","_id":"12287","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"ddc":["510"],"article_processing_charge":"No","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","quality_controlled":"1","volume":69,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Ramsay","full_name":"Dyer, Ramsay","last_name":"Dyer"},{"last_name":"Ghosh","full_name":"Ghosh, Arijit","first_name":"Arijit"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","orcid":"0000-0002-7472-2220"}],"publisher":"Springer Nature","isi":1,"month":"01","language":[{"iso":"eng"}],"external_id":{"isi":["000862193600001"]},"date_published":"2023-01-01T00:00:00Z","date_updated":"2023-08-01T12:47:32Z","day":"01"},{"quality_controlled":"1","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","article_processing_charge":"No","ddc":["570"],"publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"_id":"12421","publisher":"Portland Press","author":[{"last_name":"Fäßler","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","first_name":"Manjunath"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"scopus_import":"1","type":"journal_article","volume":51,"has_accepted_license":"1","date_published":"2023-02-01T00:00:00Z","external_id":{"isi":["000926043100001"]},"language":[{"iso":"eng"}],"month":"02","isi":1,"day":"01","date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","citation":{"ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","page":"87-99","article_type":"original","oa":1,"file":[{"creator":"dernst","access_level":"open_access","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","relation":"main_file","file_size":10045006,"date_created":"2023-03-16T07:58:16Z","checksum":"4e7069845e3dad22bb44fb71ec624c60","file_id":"12728","content_type":"application/pdf","success":1,"date_updated":"2023-03-16T07:58:16Z"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"abstract":[{"text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1042/bst20220221","file_date_updated":"2023-03-16T07:58:16Z","issue":"1","publication":"Biochemical Society Transactions","intvolume":" 51","publication_status":"published","department":[{"_id":"FlSc"}],"status":"public","keyword":["Biochemistry"],"year":"2023"},{"publication":"Journal of Fluid Mechanics","intvolume":" 954","publication_status":"published","department":[{"_id":"BjHo"}],"status":"public","year":"2023","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","date_created":"2023-01-08T23:00:53Z","citation":{"mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2023-02-02T12:34:54Z","success":1,"date_created":"2023-02-02T12:34:54Z","file_size":1931647,"relation":"main_file","access_level":"open_access","file_name":"2023_JourFluidMechanics_Marensi.pdf","creator":"dernst","file_id":"12489","checksum":"9224f987caefe5dd85a70814d3cce65c"}],"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960"}],"doi":"10.1017/jfm.2022.1001","file_date_updated":"2023-02-02T12:34:54Z","abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"date_published":"2023-01-10T00:00:00Z","language":[{"iso":"eng"}],"month":"01","isi":1,"day":"10","date_updated":"2023-08-01T12:53:23Z","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","ddc":["530"],"article_number":"A10","_id":"12105","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"author":[{"first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena"},{"orcid":"0000-0002-8490-9312","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","last_name":"Yalniz"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn"},{"orcid":"0000-0003-0423-5010","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur"}],"publisher":"Cambridge University Press","scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":954},{"issue":"1","intvolume":" 77","publication":"Evolution: International journal of organic evolution","status":"public","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2023","citation":{"ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004"},"date_created":"2023-02-05T23:00:59Z","title":"A multivariate view of the speciation continuum","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"oa_version":"Published Version","oa":1,"article_type":"original","page":"318-328","doi":"10.1093/evolut/qpac004","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"language":[{"iso":"eng"}],"external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"date_published":"2023-01-01T00:00:00Z","isi":1,"month":"01","day":"01","date_updated":"2023-08-01T12:58:30Z","pmid":1,"acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","article_processing_charge":"No","quality_controlled":"1","_id":"12514","publication_identifier":{"eissn":["1558-5646"]},"author":[{"first_name":"Daniel I.","full_name":"Bolnick, Daniel I.","last_name":"Bolnick"},{"first_name":"Amanda K.","last_name":"Hund","full_name":"Hund, Amanda K."},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"last_name":"Peng","full_name":"Peng, Foen","first_name":"Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Swapna","full_name":"Subramanian, Swapna","last_name":"Subramanian"},{"last_name":"Wolf","full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W."},{"last_name":"Yukilevich","full_name":"Yukilevich, Roman","first_name":"Roman"}],"publisher":"Oxford University Press","volume":77,"type":"journal_article","scopus_import":"1"},{"article_number":"00093","ddc":["600"],"_id":"12548","publication_identifier":{"eissn":["2375-9259"],"eisbn":["9798350346091"]},"quality_controlled":"1","article_processing_charge":"No","type":"conference","has_accepted_license":"1","author":[{"last_name":"Forghani","full_name":"Forghani, Mohammad","first_name":"Mohammad"},{"full_name":"Claramunt, Christophe","last_name":"Claramunt","first_name":"Christophe"},{"last_name":"Karimipour","full_name":"Karimipour, Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","orcid":"0000-0001-6746-4174"},{"first_name":"Georg","full_name":"Heiler, Georg","last_name":"Heiler"}],"publisher":"Institute of Electrical and Electronics Engineers","month":"02","isi":1,"external_id":{"isi":["000971492200145"]},"date_published":"2023-02-08T00:00:00Z","conference":{"name":"ICDMW: Conference on Data Mining Workshops","start_date":"2022-11-28","end_date":"2022-12-01","location":"Orlando, FL, United States"},"language":[{"iso":"eng"}],"date_updated":"2023-08-01T13:15:48Z","day":"08","oa_version":"Submitted Version","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","date_created":"2023-02-14T07:56:21Z","citation":{"ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093"},"file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-02-14T07:58:26Z","creator":"fkarimip","access_level":"open_access","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","relation":"main_file","date_created":"2023-02-14T07:58:26Z","file_size":1183339,"checksum":"c253bee25e6dfe484f96662daa119cb6","file_id":"12549"}],"file_date_updated":"2023-02-14T07:58:26Z","doi":"10.1109/icdmw58026.2022.00093","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"oa":1,"publication":"2022 IEEE International Conference on Data Mining Workshops","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"status":"public"},{"year":"2023","status":"public","department":[{"_id":"UlWa"}],"keyword":["General Mathematics","General Computer Science"],"publication_status":"published","intvolume":" 52","publication":"SIAM Journal on Computing","issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"doi":"10.1137/20m1378223","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"article_type":"original","oa":1,"page":"38-79","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2003.11351","open_access":"1"}],"oa_version":"Preprint","citation":{"short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223."},"date_created":"2023-02-16T07:03:52Z","title":"Topology and adjunction in promise constraint satisfaction","date_updated":"2023-08-01T13:11:30Z","day":"01","isi":1,"month":"01","language":[{"iso":"eng"}],"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"volume":52,"scopus_import":"1","type":"journal_article","publisher":"Society for Industrial & Applied Mathematics","author":[{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242","last_name":"Opršal","orcid":"0000-0003-1245-3456","first_name":"Jakub"},{"last_name":"Wrochna","full_name":"Wrochna, Marcin","first_name":"Marcin"},{"last_name":"Živný","full_name":"Živný, Stanislav","first_name":"Stanislav"}],"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"_id":"12563","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","article_processing_charge":"No","quality_controlled":"1"}]