[{"publication":"Frontiers in Microbiology","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["570"],"doi":"10.3389/fmicb.2021.628622","day":"12","file":[{"access_level":"open_access","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","date_created":"2021-05-11T13:05:52Z","success":1,"creator":"kschuh","file_size":14362316,"checksum":"2f856543add59273a482a7f326fc0400","content_type":"application/pdf","relation":"main_file","date_updated":"2021-05-11T13:05:52Z","file_id":"9384"}],"oa":1,"intvolume":" 12","date_published":"2021-04-12T00:00:00Z","article_number":"628622","ec_funded":1,"acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","article_type":"original","publication_identifier":{"eissn":["1664-302X"]},"year":"2021","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","author":[{"first_name":"Zaira","full_name":"Seferbekova, Zaira","last_name":"Seferbekova"},{"last_name":"Zabelkin","full_name":"Zabelkin, Alexey","first_name":"Alexey"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"first_name":"Robert","last_name":"Afasizhev","full_name":"Afasizhev, Robert"},{"first_name":"Natalia O.","last_name":"Dranenko","full_name":"Dranenko, Natalia O."},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"},{"first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","full_name":"Bochkareva, Olga"}],"date_updated":"2025-04-14T07:43:52Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2021-05-11T13:05:52Z","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","volume":12,"department":[{"_id":"FyKo"}],"publisher":"Frontiers","corr_author":"1","abstract":[{"lang":"eng","text":"Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands."}],"type":"journal_article","citation":{"ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622.","chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622.","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers, 2021, doi:10.3389/fmicb.2021.628622.","ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.628622","ieee":"Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","apa":"Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021)."},"quality_controlled":"1","_id":"9380","month":"04","scopus_import":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-05-09T22:01:38Z","external_id":{"isi":["000643713300001"]}},{"quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium."}],"type":"journal_article","citation":{"ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4). doi:10.1371/journal.pcbi.1008523","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology, vol. 17, no. 4. Public Library of Science, 2021.","apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008523.","ista":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4), e1008523.","chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523.","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021)."},"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"volume":17,"external_id":{"pmid":["33844680"],"isi":["000639711200001"]},"date_created":"2021-05-09T22:01:38Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":"1","issue":"4","month":"04","_id":"9381","ec_funded":1,"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","year":"2021","article_type":"original","article_number":"e1008523","intvolume":" 17","date_published":"2021-04-01T00:00:00Z","doi":"10.1371/journal.pcbi.1008523","day":"01","oa":1,"file":[{"file_size":1323820,"creator":"kschuh","date_created":"2021-05-11T13:50:06Z","success":1,"file_name":"2021_pcbi_Kleshnina.pdf","access_level":"open_access","file_id":"9385","date_updated":"2021-05-11T13:50:06Z","relation":"main_file","checksum":"a94ebe0c4116f5047eaa6029e54d2dac","content_type":"application/pdf"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"publication":"PLoS Computational Biology","isi":1,"oa_version":"Published Version","file_date_updated":"2021-05-11T13:50:06Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-06-12T06:40:39Z","title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","author":[{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Sabrina S.","last_name":"Streipert","full_name":"Streipert, Sabrina S."},{"first_name":"Jerzy A.","last_name":"Filar","full_name":"Filar, Jerzy A."},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}]},{"publication":"Evolution","isi":1,"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 75","date_published":"2021-03-22T00:00:00Z","doi":"10.1111/evo.14215","day":"22","oa":1,"file":[{"file_id":"10921","date_updated":"2022-03-25T12:02:04Z","relation":"main_file","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","content_type":"application/pdf","file_size":719991,"creator":"kschuh","success":1,"date_created":"2022-03-25T12:02:04Z","file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"year":"2021","article_type":"original","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","page":"1256-1273","date_updated":"2023-10-18T08:16:01Z","title":"Defining the speciation continuum","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"}],"file_date_updated":"2022-03-25T12:02:04Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","department":[{"_id":"NiBa"}],"volume":75,"publisher":"Oxford University Press","quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us."}],"citation":{"ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273."},"_id":"9383","scopus_import":"1","issue":"6","month":"03","date_created":"2021-05-09T22:01:39Z","publication_status":"published","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"external_id":{"isi":["000647226400001"]}},{"external_id":{"pmid":["33901507"],"isi":["000659161500002"]},"date_created":"2021-05-12T05:58:42Z","publication_status":"published","scopus_import":"1","month":"04","_id":"9387","quality_controlled":"1","citation":{"chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.","apa":"Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021)."},"abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"type":"journal_article","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"publisher":"Elsevier ","department":[{"_id":"GradSch"}],"volume":524,"keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-06-12T06:40:55Z","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","author":[{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","orcid":"0000-0002-6246-1465","first_name":"Kseniia"},{"full_name":"Neretina, Tatiana Yu.","last_name":"Neretina","first_name":"Tatiana Yu."},{"full_name":"Kondrashov, Alexey S.","last_name":"Kondrashov","first_name":"Alexey S."}],"article_type":"original","year":"2021","publication_identifier":{"issn":["0022-5193"]},"acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","article_number":"110729","date_published":"2021-04-24T00:00:00Z","intvolume":" 524","oa":1,"day":"24","doi":"10.1016/j.jtbi.2021.110729","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Journal of Theoretical Biology"},{"oa_version":"Published Version","date_created":"2021-05-14T12:07:53Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"_id":"9389","date_updated":"2025-06-12T06:32:43Z","contributor":[{"first_name":"Marco","contributor_type":"contact_person","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini"}],"related_material":{"record":[{"id":"8910","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-05-14T11:56:48Z","status":"public","date_published":"2021-01-01T00:00:00Z","citation":{"short":"M. Valentini, (2021).","mla":"Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.","chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389"},"file":[{"date_created":"2021-05-14T11:42:23Z","file_name":"Notebook_Valentini.pdf","file_size":10572981,"creator":"mvalenti","access_level":"open_access","file_id":"9390","date_updated":"2021-05-14T11:42:23Z","relation":"main_file","checksum":"80a905c4eef24dab6fb247e81a3d67f5","content_type":"application/pdf"},{"access_level":"open_access","date_created":"2021-05-14T11:56:48Z","file_name":"Experimental_data.zip","creator":"mvalenti","file_size":99076111,"checksum":"1e61a7e63949448a8db0091cdac23570","content_type":"application/x-zip-compressed","relation":"main_file","date_updated":"2021-05-14T11:56:48Z","file_id":"9391"}],"oa":1,"doi":"10.15479/AT:ISTA:9389","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"type":"research_data","year":"2021","acknowledged_ssus":[{"_id":"NanoFab"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"ddc":["530"],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2021","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","article_type":"original","publication_identifier":{"issn":["0925-9856"],"eissn":["1572-8102"]},"ec_funded":1,"date_published":"2021-09-01T00:00:00Z","intvolume":" 57","oa":1,"doi":"10.1007/s10703-021-00373-5","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication":"Formal Methods in System Design","arxiv":1,"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","page":"401-428","date_updated":"2025-04-15T07:23:30Z","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus"},{"first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design, vol. 57, Springer, 2021, pp. 401–28, doi:10.1007/s10703-021-00373-5.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design. Springer, 2021. https://doi.org/10.1007/s10703-021-00373-5.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 2021;57:401-428. doi:10.1007/s10703-021-00373-5","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” Formal Methods in System Design, vol. 57. Springer, pp. 401–428, 2021.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-021-00373-5","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428."},"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"main_file_link":[{"url":"https://arxiv.org/abs/1504.07384","open_access":"1"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"volume":57,"external_id":{"arxiv":["1504.07384"],"isi":["000645490300001"]},"date_created":"2021-05-16T22:01:47Z","publication_status":"published","scopus_import":"1","month":"09","_id":"9393"},{"date_created":"2021-05-19T12:25:42Z","oa_version":"Published Version","editor":[{"first_name":"Ralph","full_name":"Hertwig, Ralph","last_name":"Hertwig"},{"last_name":"Engel","full_name":"Engel, Christoph","first_name":"Christoph"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","month":"03","_id":"9403","date_updated":"2023-02-23T13:57:04Z","page":"139-152","author":[{"orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"}],"title":"The evolution of strategic ignorance in strategic interaction","year":"2021","publication_identifier":{"isbn":["978-0-262-04559-9"]},"intvolume":" 29","quality_controlled":"1","date_published":"2021-03-01T00:00:00Z","abstract":[{"text":"Optimal decision making requires individuals to know their available options and to anticipate correctly what consequences these options have. In many social interactions, however, we refrain from gathering all relevant information, even if this information would help us make better decisions and is costless to obtain. This chapter examines several examples of “deliberate ignorance.” Two simple models are proposed to illustrate how ignorance can evolve among self-interested and payoff - maximizing individuals, and open problems are highlighted that lie ahead for future research to explore.","lang":"eng"}],"day":"01","type":"book_chapter","citation":{"mla":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” Deliberate Ignorance: Choosing Not To Know, edited by Ralph Hertwig and Christoph Engel, vol. 29, MIT Press, 2021, pp. 139–52.","ista":"Schmid L, Hilbe C. 2021.The evolution of strategic ignorance in strategic interaction. In: Deliberate Ignorance: Choosing Not To Know. vol. 29, 139–152.","chicago":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” In Deliberate Ignorance: Choosing Not To Know, edited by Ralph Hertwig and Christoph Engel, 29:139–52. Strüngmann Forum Reports. MIT Press, 2021.","ama":"Schmid L, Hilbe C. The evolution of strategic ignorance in strategic interaction. In: Hertwig R, Engel C, eds. Deliberate Ignorance: Choosing Not To Know. Vol 29. Strüngmann Forum Reports. MIT Press; 2021:139-152.","apa":"Schmid, L., & Hilbe, C. (2021). The evolution of strategic ignorance in strategic interaction. In R. Hertwig & C. Engel (Eds.), Deliberate Ignorance: Choosing Not To Know (Vol. 29, pp. 139–152). MIT Press.","ieee":"L. Schmid and C. Hilbe, “The evolution of strategic ignorance in strategic interaction,” in Deliberate Ignorance: Choosing Not To Know, vol. 29, R. Hertwig and C. Engel, Eds. MIT Press, 2021, pp. 139–152.","short":"L. Schmid, C. Hilbe, in:, R. Hertwig, C. Engel (Eds.), Deliberate Ignorance: Choosing Not To Know, MIT Press, 2021, pp. 139–152."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://esforum.de/publications/PDFs/sfr29/SFR29_09_Hilbe%20and%20Schmid.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"MIT Press","publication":"Deliberate Ignorance: Choosing Not To Know","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"volume":29,"series_title":"Strüngmann Forum Reports"},{"external_id":{"pmid":["31804937"],"isi":["000649620700009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-05-23T22:01:42Z","month":"06","scopus_import":"1","issue":"6","_id":"9408","citation":{"short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.","ista":"Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895."},"abstract":[{"text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype.","lang":"eng"}],"pmid":1,"type":"journal_article","quality_controlled":"1","publisher":"IEEE","volume":27,"department":[{"_id":"BeBi"}],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-05-25T15:08:49Z","author":[{"full_name":"Feng, Xudong","last_name":"Feng","first_name":"Xudong"},{"last_name":"Liu","full_name":"Liu, Jiafeng","first_name":"Jiafeng"},{"first_name":"Huamin","full_name":"Wang, Huamin","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Yin","first_name":"Yin"},{"full_name":"Bao, Hujun","last_name":"Bao","first_name":"Hujun"},{"first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"title":"Computational design of skinned Quad-Robots","date_updated":"2025-07-10T12:01:44Z","article_number":"2881-2895","year":"2021","acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","publication_identifier":{"issn":["1941-0506"],"eissn":["1077-2626"]},"ec_funded":1,"oa":1,"file":[{"checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","content_type":"application/pdf","relation":"main_file","date_updated":"2021-05-25T15:08:49Z","file_id":"9427","access_level":"open_access","date_created":"2021-05-25T15:08:49Z","file_name":"2021_TVCG_Feng.pdf","success":1,"creator":"kschuh","file_size":6183002}],"day":"01","doi":"10.1109/TVCG.2019.2957218","date_published":"2021-06-01T00:00:00Z","intvolume":" 27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"ddc":["000"],"isi":1,"publication":"IEEE Transactions on Visualization and Computer Graphics"},{"volume":44,"department":[{"_id":"ScWa"}],"publisher":"Springer","type":"journal_article","abstract":[{"text":"The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.","lang":"eng"}],"citation":{"short":"A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2","ista":"Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59.","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2."},"quality_controlled":"1","_id":"9411","month":"04","issue":"4","scopus_import":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-05-23T22:01:44Z","external_id":{"isi":["000643251300001"]},"publication":"European Physical Journal E","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"day":"24","doi":"10.1140/epje/s10189-021-00065-2","file":[{"access_level":"open_access","success":1,"file_name":"2021_EPJE_Sukhov.pdf","date_created":"2021-05-25T11:32:14Z","file_size":2507870,"creator":"kschuh","relation":"main_file","content_type":"application/pdf","checksum":"0ef342d011afbe3c5cb058fda9a3f395","file_id":"9422","date_updated":"2021-05-25T11:32:14Z"}],"oa":1,"intvolume":" 44","date_published":"2021-04-24T00:00:00Z","article_number":"59","acknowledgement":"This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time.","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"year":"2021","author":[{"full_name":"Sukhov, Alexander","last_name":"Sukhov","first_name":"Alexander"},{"last_name":"Hubert","full_name":"Hubert, Maxime","first_name":"Maxime"},{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","last_name":"Grosjean","orcid":"0000-0001-5154-417X","first_name":"Galien M"},{"first_name":"Oleg","full_name":"Trosman, Oleg","last_name":"Trosman"},{"first_name":"Sebastian","full_name":"Ziegler, Sebastian","last_name":"Ziegler"},{"first_name":"Ylona","full_name":"Collard, Ylona","last_name":"Collard"},{"first_name":"Nicolas","last_name":"Vandewalle","full_name":"Vandewalle, Nicolas"},{"first_name":"Ana Sunčana","full_name":"Smith, Ana Sunčana","last_name":"Smith"},{"last_name":"Harting","full_name":"Harting, Jens","first_name":"Jens"}],"title":"Regimes of motion of magnetocapillary swimmers","date_updated":"2025-07-10T12:01:45Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2021-05-25T11:32:14Z","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version"},{"date_published":"2021-04-19T00:00:00Z","intvolume":" 32","oa":1,"doi":"10.1091/MBC.E20-11-0723","day":"19","year":"2021","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","article_type":"original","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"ec_funded":1,"isi":1,"publication":"Molecular Biology of the Cell","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","page":"869-879","date_updated":"2025-04-14T07:21:30Z","author":[{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke"},{"first_name":"Franziska","full_name":"Decker, Franziska","last_name":"Decker"},{"last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","first_name":"Paulo R"},{"full_name":"Pelletier, James F.","last_name":"Pelletier","first_name":"James F."},{"full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin"},{"last_name":"Brugués","full_name":"Brugués, Jan","first_name":"Jan"},{"first_name":"Timothy J.","last_name":"Mitchison","full_name":"Mitchison, Timothy J."}],"title":"Spatial variation of microtubule depolymerization in large asters","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","citation":{"mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879."},"pmid":1,"type":"journal_article","abstract":[{"text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.","lang":"eng"}],"department":[{"_id":"MaLo"}],"volume":32,"main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"publisher":"American Society for Cell Biology","date_created":"2021-05-23T22:01:45Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (3.0)"},"publication_status":"published","external_id":{"isi":["000641574700005"],"pmid":["33439671"]},"_id":"9414","issue":"9","scopus_import":"1","month":"04"},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_number":"3226","publication_identifier":{"eissn":["2041-1723"]},"year":"2021","article_type":"original","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","doi":"10.1038/s41467-021-23506-0","day":"28","file":[{"file_id":"9538","date_updated":"2021-06-09T15:21:14Z","relation":"main_file","checksum":"53ccc53d09a9111143839dbe7784e663","content_type":"application/pdf","file_size":6166295,"creator":"kschuh","file_name":"2021_NatureCommunications_Obr.pdf","date_created":"2021-06-09T15:21:14Z","success":1,"access_level":"open_access"}],"oa":1,"intvolume":" 12","date_published":"2021-05-28T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"ddc":["570"],"publication":"Nature Communications","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2021-06-09T15:21:14Z","has_accepted_license":"1","article_processing_charge":"No","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","author":[{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr","first_name":"Martin"},{"first_name":"Clifton L.","last_name":"Ricana","full_name":"Ricana, Clifton L."},{"full_name":"Nikulin, Nadia","last_name":"Nikulin","first_name":"Nadia"},{"first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R.","last_name":"Feathers"},{"first_name":"Marco","full_name":"Klanschnig, Marco","last_name":"Klanschnig"},{"first_name":"Andreas","full_name":"Thader, Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"first_name":"Volker M.","full_name":"Vogt, Volker M.","last_name":"Vogt"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."}],"date_updated":"2025-04-15T08:24:49Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"type":"journal_article","abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"citation":{"mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021)."},"quality_controlled":"1","publisher":"Nature Research","corr_author":"1","volume":12,"department":[{"_id":"FlSc"}],"external_id":{"isi":["000659145000011"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-05-28T14:25:50Z","month":"05","issue":"1","scopus_import":"1","_id":"9431"},{"date_updated":"2025-01-22T08:09:40Z","title":"Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles","author":[{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim"},{"first_name":"Edmond","orcid":"0000-0003-2640-4049","full_name":"Koudjinan, Edmond","last_name":"Koudjinan","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E"}],"file_date_updated":"2021-05-30T13:57:37Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"arXiv","arxiv":1,"OA_place":"repository","ddc":["500"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-07T00:00:00Z","doi":"10.48550/arXiv.2107.03499","day":"07","oa":1,"file":[{"creator":"ekoudjin","file_size":353431,"date_created":"2021-05-30T13:57:37Z","file_name":"CoExistence 2&3 caustics 3_17_6_2_3.pdf","access_level":"open_access","date_updated":"2021-05-30T13:57:37Z","file_id":"9436","content_type":"application/pdf","checksum":"b281b5c2e3e90de0646c3eafcb2c6c25","relation":"main_file"}],"year":"2021","article_number":"2107.03499","_id":"9435","month":"07","date_created":"2021-05-30T13:58:13Z","publication_status":"submitted","external_id":{"arxiv":["2107.03499"]},"department":[{"_id":"VaKa"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.03499","open_access":"1"}],"corr_author":"1","type":"preprint","abstract":[{"lang":"eng","text":"For any given positive integer l, we prove that every plane deformation of a circlewhich preserves the 1/2and 1/ (2l + 1) -rational caustics is trivial i.e. the deformationconsists only of similarities (rescalings and isometries)."}],"citation":{"short":"V. Kaloshin, E. Koudjinan, ArXiv (n.d.).","ieee":"V. Kaloshin and E. Koudjinan, “Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles,” arXiv. .","ama":"Kaloshin V, Koudjinan E. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles. arXiv. doi:10.48550/arXiv.2107.03499","apa":"Kaloshin, V., & Koudjinan, E. (n.d.). Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles. arXiv. https://doi.org/10.48550/arXiv.2107.03499","ista":"Kaloshin V, Koudjinan E. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles. arXiv, 2107.03499.","chicago":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.03499.","mla":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles.” ArXiv, 2107.03499, doi:10.48550/arXiv.2107.03499."}},{"quality_controlled":"1","abstract":[{"text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0"},"department":[{"_id":"GaTk"}],"volume":24,"main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"publisher":"Springer Nature","date_created":"2021-05-30T22:01:24Z","publication_status":"published","external_id":{"pmid":["34017131"],"isi":["000652577300003"]},"_id":"9439","scopus_import":"1","month":"05","intvolume":" 24","date_published":"2021-05-20T00:00:00Z","day":"20","doi":"10.1038/s41593-021-00846-0","oa":1,"ec_funded":1,"year":"2021","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"article_type":"original","publication":"Nature Neuroscience","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Preprint","page":"998-1009","date_updated":"2025-06-12T06:41:38Z","title":"Efficient and adaptive sensory codes","author":[{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"last_name":"Hermundstad","full_name":"Hermundstad, Ann M.","first_name":"Ann M."}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"publication_identifier":{"isbn":["978-3-95977-184-9"],"issn":["1868-8969"]},"year":"2021","acknowledgement":"We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge the reviewers.","ec_funded":1,"file":[{"date_updated":"2021-06-02T10:22:33Z","file_id":"9442","content_type":"application/pdf","checksum":"c322aa48d5d35a35877896cc565705b6","relation":"main_file","success":1,"file_name":"LIPIcs-SoCG-2021-17.pdf","date_created":"2021-06-02T10:22:33Z","creator":"mwintrae","file_size":1972902,"access_level":"open_access"}],"oa":1,"doi":"10.4230/LIPIcs.SoCG.2021.17","day":"02","date_published":"2021-06-02T00:00:00Z","intvolume":" 189","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","ddc":["005","516","514"],"series_title":"Leibniz International Proceedings in Informatics (LIPIcs)","publication":"37th International Symposium on Computational Geometry (SoCG 2021)","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-06-02T10:22:33Z","title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations","author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel"},{"full_name":"Kachanovich, Siargey","last_name":"Kachanovich","first_name":"Siargey"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220"}],"related_material":{"record":[{"status":"public","id":"12960","relation":"later_version"}]},"date_updated":"2025-04-15T07:09:18Z","page":"17:1-17:16","citation":{"apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In 37th International Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.17","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th International Symposium on Computational Geometry (SoCG 2021). Vol 189. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,” in 37th International Symposium on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 17:1-17:16.","mla":"Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium on Computational Geometry (SoCG 2021), vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol. 189, 17:1-17:16.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” In 37th International Symposium on Computational Geometry (SoCG 2021), 189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2021, p. 17:1-17:16."},"type":"conference","abstract":[{"text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. ","lang":"eng"}],"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":189,"department":[{"_id":"HeEd"}],"conference":{"end_date":"2021-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Virtual","start_date":"2021-06-07"},"alternative_title":["LIPIcs"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-06-02T10:10:55Z","month":"06","place":"Dagstuhl, Germany","scopus_import":"1","_id":"9441"},{"status":"public","language":[{"iso":"eng"}],"file_date_updated":"2021-10-14T13:36:38Z","has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Ruiz-Lopez","full_name":"Ruiz-Lopez, N","first_name":"N"},{"first_name":"J","full_name":"Pérez-Sancho, J","last_name":"Pérez-Sancho"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"first_name":"RP","full_name":"Haslam, RP","last_name":"Haslam"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Catalá","full_name":"Catalá, R","first_name":"R"},{"first_name":"C","full_name":"Perea-Resa, C","last_name":"Perea-Resa"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"S","full_name":"García-Hernández, S","last_name":"García-Hernández"},{"last_name":"Albert","full_name":"Albert, A","first_name":"A"},{"first_name":"J","last_name":"Vallarino","full_name":"Vallarino, J"},{"first_name":"J","last_name":"Lin","full_name":"Lin, J"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Macho, AP","last_name":"Macho","first_name":"AP"},{"last_name":"Salinas","full_name":"Salinas, J","first_name":"J"},{"first_name":"A","last_name":"Rosado","full_name":"Rosado, A"},{"full_name":"Napier, JA","last_name":"Napier","first_name":"JA"},{"full_name":"Amorim-Silva, V","last_name":"Amorim-Silva","first_name":"V"},{"first_name":"MA","full_name":"Botella, MA","last_name":"Botella"}],"title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","date_updated":"2025-04-14T07:45:00Z","page":"2431-2453","oa_version":"Published Version","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580"],"publication":"Plant Cell","isi":1,"ec_funded":1,"article_type":"original","acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"year":"2021","day":"01","doi":"10.1093/plcell/koab122","oa":1,"file":[{"relation":"main_file","checksum":"22d596678d00310d793611864a6d0fcd","content_type":"application/pdf","file_id":"10141","date_updated":"2021-10-14T13:36:38Z","access_level":"open_access","date_created":"2021-10-14T13:36:38Z","file_name":"2021_PlantCell_RuizLopez.pdf","success":1,"file_size":2952028,"creator":"cchlebak"}],"intvolume":" 33","date_published":"2021-07-01T00:00:00Z","month":"07","issue":"7","scopus_import":"1","_id":"9443","external_id":{"isi":["000703938100026"],"pmid":["33944955"]},"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"date_created":"2021-06-02T13:13:58Z","publisher":"American Society of Plant Biologists","volume":33,"department":[{"_id":"JiFr"}],"pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress."}],"citation":{"short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453.","chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021."},"quality_controlled":"1"},{"external_id":{"isi":["000657724200001"]},"date_created":"2021-06-03T09:58:38Z","publication_status":"published","scopus_import":"1","issue":"5","month":"05","_id":"9447","quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) based water-in-salt electrolytes (WiSEs) has recently emerged as a new promising class of electrolytes, primarily owing to their wide electrochemical stability windows (~3–4 V), that by far exceed the thermodynamic stability window of water (1.23 V). Upon increasing the salt concentration towards superconcentration the onset of the oxygen evolution reaction (OER) shifts more significantly than the hydrogen evolution reaction (HER) does. The OER shift has been explained by the accumulation of hydrophobic anions blocking water access to the electrode surface, hence by double layer theory. Here we demonstrate that the processes during oxidation are much more complex, involving OER, carbon and salt decomposition by OER intermediates, and salt precipitation upon local oversaturation. The positive shift in the onset potential of oxidation currents was elucidated by combining several advanced analysis techniques: rotating ring-disk electrode voltammetry, online electrochemical mass spectrometry, and X-ray photoelectron spectroscopy, using both dilute and superconcentrated electrolytes. The results demonstrate the importance of reactive OER intermediates and surface films for electrolyte and electrode stability and motivate further studies of the nature of the electrode."}],"citation":{"apa":"Maffre, M., Bouchal, R., Freunberger, S. A., Lindahl, N., Johansson, P., Favier, F., … Bélanger, D. (2021). Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. IOP Publishing. https://doi.org/10.1149/1945-7111/ac0300","ieee":"M. Maffre et al., “Investigation of electrochemical and chemical processes occurring at positive potentials in ‘Water-in-Salt’ electrolytes,” Journal of The Electrochemical Society, vol. 168, no. 5. IOP Publishing, 2021.","ama":"Maffre M, Bouchal R, Freunberger SA, et al. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 2021;168(5). doi:10.1149/1945-7111/ac0300","ista":"Maffre M, Bouchal R, Freunberger SA, Lindahl N, Johansson P, Favier F, Fontaine O, Bélanger D. 2021. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 168(5), 050550.","chicago":"Maffre, Marion, Roza Bouchal, Stefan Alexander Freunberger, Niklas Lindahl, Patrik Johansson, Frédéric Favier, Olivier Fontaine, and Daniel Bélanger. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society. IOP Publishing, 2021. https://doi.org/10.1149/1945-7111/ac0300.","mla":"Maffre, Marion, et al. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society, vol. 168, no. 5, 050550, IOP Publishing, 2021, doi:10.1149/1945-7111/ac0300.","short":"M. Maffre, R. Bouchal, S.A. Freunberger, N. Lindahl, P. Johansson, F. Favier, O. Fontaine, D. Bélanger, Journal of The Electrochemical Society 168 (2021)."},"publisher":"IOP Publishing","department":[{"_id":"StFr"}],"volume":168,"keyword":["Renewable Energy","Sustainability and the Environment","Electrochemistry","Materials Chemistry","Electronic","Optical and Magnetic Materials","Surfaces","Coatings and Films","Condensed Matter Physics"],"oa_version":"None","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-21T06:02:10Z","author":[{"last_name":"Maffre","full_name":"Maffre, Marion","first_name":"Marion"},{"last_name":"Bouchal","full_name":"Bouchal, Roza","first_name":"Roza"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"},{"first_name":"Niklas","last_name":"Lindahl","full_name":"Lindahl, Niklas"},{"first_name":"Patrik","full_name":"Johansson, Patrik","last_name":"Johansson"},{"last_name":"Favier","full_name":"Favier, Frédéric","first_name":"Frédéric"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"},{"first_name":"Daniel","last_name":"Bélanger","full_name":"Bélanger, Daniel"}],"title":"Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes","year":"2021","publication_identifier":{"issn":["0013-4651"],"eissn":["1945-7111"]},"article_number":"050550","intvolume":" 168","date_published":"2021-05-01T00:00:00Z","doi":"10.1149/1945-7111/ac0300","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of The Electrochemical Society","isi":1},{"external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"publication_status":"published","date_created":"2021-06-06T22:01:28Z","month":"09","scopus_import":"1","issue":"6","_id":"9462","citation":{"short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096"},"abstract":[{"text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.00992"}],"volume":281,"department":[{"_id":"RoSe"}],"oa_version":"Preprint","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Andreas","full_name":"Deuchert, Andreas","last_name":"Deuchert"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","date_updated":"2025-04-14T07:26:53Z","article_number":"109096","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","year":"2021","article_type":"original","ec_funded":1,"oa":1,"day":"15","doi":"10.1016/j.jfa.2021.109096","date_published":"2021-09-15T00:00:00Z","intvolume":" 281","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"arxiv":1,"publication":"Journal of Functional Analysis"},{"publisher":"IEEE","department":[{"_id":"GeKa"}],"quality_controlled":"1","abstract":[{"text":"We firstly introduce the self-assembled growth of highly uniform Ge quantum wires with controllable position, distance and length on patterned Si (001) substrates. We then present the electrically tunable strong spin-orbit coupling, the first Ge hole spin qubit and ultrafast operation of hole spin qubit in the Ge/Si quantum wires.","lang":"eng"}],"type":"conference","citation":{"apa":"Gao, F., Zhang, J. Y., Wang, J. H., Ming, M., Wang, T., Zhang, J. J., … Guo, G. P. (2021). Ge/Si quantum wires for quantum computing. In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. Virtual, Online: IEEE. https://doi.org/10.1109/EDTM50988.2021.9420817","ama":"Gao F, Zhang JY, Wang JH, et al. Ge/Si quantum wires for quantum computing. In: 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE; 2021. doi:10.1109/EDTM50988.2021.9420817","ieee":"F. Gao et al., “Ge/Si quantum wires for quantum computing,” in 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, Virtual, Online, 2021.","ista":"Gao F, Zhang JY, Wang JH, Ming M, Wang T, Zhang JJ, Watzinger H, Kukucka J, Vukušić L, Katsaros G, Wang K, Xu G, Li HO, Guo GP. 2021. Ge/Si quantum wires for quantum computing. 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. EDTM: IEEE Electron Devices Technology and Manufacturing Conference, 9420817.","chicago":"Gao, Fei, Jie Yin Zhang, Jian Huan Wang, Ming Ming, Tina Wang, Jian Jun Zhang, Hannes Watzinger, et al. “Ge/Si Quantum Wires for Quantum Computing.” In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE, 2021. https://doi.org/10.1109/EDTM50988.2021.9420817.","mla":"Gao, Fei, et al. “Ge/Si Quantum Wires for Quantum Computing.” 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, 9420817, IEEE, 2021, doi:10.1109/EDTM50988.2021.9420817.","short":"F. Gao, J.Y. Zhang, J.H. Wang, M. Ming, T. Wang, J.J. Zhang, H. Watzinger, J. Kukucka, L. Vukušić, G. Katsaros, K. Wang, G. Xu, H.O. Li, G.P. Guo, in:, 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, IEEE, 2021."},"scopus_import":"1","month":"04","_id":"9464","external_id":{"isi":["000675595800006"]},"conference":{"end_date":"2021-04-11","start_date":"2021-04-08","name":"EDTM: IEEE Electron Devices Technology and Manufacturing Conference","location":"Virtual, Online"},"date_created":"2021-06-06T22:01:29Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021","isi":1,"ec_funded":1,"year":"2021","publication_identifier":{"isbn":["9781728181769"]},"acknowledgement":"This work was supported by the National Key R&D Program of China (Grant No. 2016YFA0301700) and the ERC Starting Grant no. 335497.","article_number":"9420817","date_published":"2021-04-08T00:00:00Z","day":"08","doi":"10.1109/EDTM50988.2021.9420817","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2024-10-22T09:41:03Z","title":"Ge/Si quantum wires for quantum computing","author":[{"first_name":"Fei","full_name":"Gao, Fei","last_name":"Gao"},{"first_name":"Jie Yin","last_name":"Zhang","full_name":"Zhang, Jie Yin"},{"last_name":"Wang","full_name":"Wang, Jian Huan","first_name":"Jian Huan"},{"first_name":"Ming","full_name":"Ming, Ming","last_name":"Ming"},{"first_name":"Tina","last_name":"Wang","full_name":"Wang, Tina"},{"first_name":"Jian Jun","full_name":"Zhang, Jian Jun","last_name":"Zhang"},{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip"},{"orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios"},{"full_name":"Wang, Ke","last_name":"Wang","first_name":"Ke"},{"full_name":"Xu, Gang","last_name":"Xu","first_name":"Gang"},{"first_name":"Hai Ou","last_name":"Li","full_name":"Li, Hai Ou"},{"first_name":"Guo Ping","full_name":"Guo, Guo Ping","last_name":"Guo"}],"oa_version":"None"},{"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2021-06-11T13:16:26Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-07-10T12:01:46Z","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton","last_name":"Nikitenko"},{"orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","full_name":"Osang, Georg F","first_name":"Georg F"}],"title":"A step in the Delaunay mosaic of order k","year":"2021","article_type":"original","publication_identifier":{"eissn":["1420-8997"],"issn":["0047-2468"]},"article_number":"15","date_published":"2021-04-01T00:00:00Z","intvolume":" 112","file":[{"creator":"kschuh","file_size":694706,"date_created":"2021-06-11T13:16:26Z","file_name":"2021_Geometry_Edelsbrunner.pdf","success":1,"access_level":"open_access","date_updated":"2021-06-11T13:16:26Z","file_id":"9544","checksum":"e52a832f1def52a2b23d21bcc09e646f","content_type":"application/pdf","relation":"main_file"}],"oa":1,"doi":"10.1007/s00022-021-00577-4","day":"01","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Geometry","date_created":"2021-06-06T22:01:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","scopus_import":"1","issue":"1","month":"04","_id":"9465","quality_controlled":"1","citation":{"short":"H. Edelsbrunner, A. Nikitenko, G.F. Osang, Journal of Geometry 112 (2021).","ista":"Edelsbrunner H, Nikitenko A, Osang GF. 2021. A step in the Delaunay mosaic of order k. Journal of Geometry. 112(1), 15.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Georg F Osang. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00022-021-00577-4.","mla":"Edelsbrunner, Herbert, et al. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry, vol. 112, no. 1, 15, Springer Nature, 2021, doi:10.1007/s00022-021-00577-4.","ama":"Edelsbrunner H, Nikitenko A, Osang GF. A step in the Delaunay mosaic of order k. Journal of Geometry. 2021;112(1). doi:10.1007/s00022-021-00577-4","ieee":"H. Edelsbrunner, A. Nikitenko, and G. F. Osang, “A step in the Delaunay mosaic of order k,” Journal of Geometry, vol. 112, no. 1. Springer Nature, 2021.","apa":"Edelsbrunner, H., Nikitenko, A., & Osang, G. F. (2021). A step in the Delaunay mosaic of order k. Journal of Geometry. Springer Nature. https://doi.org/10.1007/s00022-021-00577-4"},"abstract":[{"text":"Given a locally finite set 𝑋⊆ℝ𝑑 and an integer 𝑘≥0, we consider the function 𝐰𝑘:Del𝑘(𝑋)→ℝ on the dual of the order-k Voronoi tessellation, whose sublevel sets generalize the notion of alpha shapes from order-1 to order-k (Edelsbrunner et al. in IEEE Trans Inf Theory IT-29:551–559, 1983; Krasnoshchekov and Polishchuk in Inf Process Lett 114:76–83, 2014). While this function is not necessarily generalized discrete Morse, in the sense of Forman (Adv Math 134:90–145, 1998) and Freij (Discrete Math 309:3821–3829, 2009), we prove that it satisfies similar properties so that its increments can be meaningfully classified into critical and non-critical steps. This result extends to the case of weighted points and sheds light on k-fold covers with balls in Euclidean space.","lang":"eng"}],"type":"journal_article","corr_author":"1","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"volume":112},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"arxiv":1,"publication":"Journal of Fluid Mechanics","isi":1,"article_number":"A17","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"year":"2021","acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","article_type":"original","doi":"10.1017/jfm.2021.371","day":"25","file":[{"date_updated":"2021-08-03T09:53:28Z","file_id":"9766","content_type":"application/pdf","checksum":"867ad077e45c181c2c5ec1311ba27c41","relation":"main_file","creator":"kschuh","file_size":4087358,"file_name":"2021_JournalFluidMechanics_Marensi.pdf","date_created":"2021-08-03T09:53:28Z","success":1,"access_level":"open_access"}],"oa":1,"intvolume":" 919","date_published":"2021-07-25T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2021-08-03T09:53:28Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Elena","orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","full_name":"Marensi, Elena"},{"full_name":"He, Shuisheng","last_name":"He","first_name":"Shuisheng"},{"last_name":"Willis","full_name":"Willis, Ashley P.","first_name":"Ashley P."}],"title":"Suppression of turbulence and travelling waves in a vertical heated pipe","date_updated":"2025-07-10T12:01:47Z","oa_version":"Published Version","publisher":"Cambridge University Press","corr_author":"1","volume":919,"department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation."}],"type":"journal_article","citation":{"short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371.","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371"},"quality_controlled":"1","month":"07","scopus_import":"1","_id":"9467","external_id":{"arxiv":["2008.13486"],"isi":["000653785000001"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-06-06T22:01:30Z"}]