[{"publication_identifier":{"eissn":["1664-302X"]},"ec_funded":1,"month":"04","year":"2021","date_updated":"2025-04-14T07:43:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9380","day":"12","article_number":"628622","date_published":"2021-04-12T00:00:00Z","doi":"10.3389/fmicb.2021.628622","intvolume":"        12","publication":"Frontiers in Microbiology","acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"ieee":"Z. Seferbekova <i>et al.</i>, “High rates of genome rearrangements and pathogenicity of Shigella spp,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.","ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers in Microbiology</i>, vol. 12, 628622, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>.","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.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>.","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. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>","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."},"ddc":["570"],"volume":12,"isi":1,"department":[{"_id":"FyKo"}],"publisher":"Frontiers","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"author":[{"first_name":"Zaira","last_name":"Seferbekova","full_name":"Seferbekova, Zaira"},{"full_name":"Zabelkin, Alexey","last_name":"Zabelkin","first_name":"Alexey"},{"last_name":"Yakovleva","first_name":"Yulia","full_name":"Yakovleva, Yulia"},{"first_name":"Robert","last_name":"Afasizhev","full_name":"Afasizhev, Robert"},{"full_name":"Dranenko, Natalia O.","first_name":"Natalia O.","last_name":"Dranenko"},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva"}],"corr_author":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","has_accepted_license":"1","status":"public","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","article_processing_charge":"No","date_created":"2021-05-09T22:01:38Z","publication_status":"published","oa_version":"Published Version","article_type":"original","file_date_updated":"2021-05-11T13:05:52Z","external_id":{"isi":["000643713300001"]},"abstract":[{"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.","lang":"eng"}],"file":[{"file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","relation":"main_file","content_type":"application/pdf","creator":"kschuh","checksum":"2f856543add59273a482a7f326fc0400","access_level":"open_access","date_created":"2021-05-11T13:05:52Z","success":1,"date_updated":"2021-05-11T13:05:52Z","file_size":14362316,"file_id":"9384"}]},{"isi":1,"department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","author":[{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Streipert, Sabrina S.","first_name":"Sabrina S.","last_name":"Streipert"},{"full_name":"Filar, Jerzy A.","first_name":"Jerzy A.","last_name":"Filar"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"status":"public","has_accepted_license":"1","article_processing_charge":"No","title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","oa_version":"Published Version","date_created":"2021-05-09T22:01:38Z","publication_status":"published","issue":"4","file_date_updated":"2021-05-11T13:50:06Z","article_type":"original","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000639711200001"],"pmid":["33844680"]},"file":[{"date_updated":"2021-05-11T13:50:06Z","file_id":"9385","file_size":1323820,"file_name":"2021_pcbi_Kleshnina.pdf","content_type":"application/pdf","relation":"main_file","creator":"kschuh","access_level":"open_access","success":1,"date_created":"2021-05-11T13:50:06Z","checksum":"a94ebe0c4116f5047eaa6029e54d2dac"}],"pmid":1,"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"ec_funded":1,"month":"04","year":"2021","date_updated":"2025-06-12T06:40:39Z","_id":"9381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","date_published":"2021-04-01T00:00:00Z","article_number":"e1008523","doi":"10.1371/journal.pcbi.1008523","acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","publication":"PLoS Computational Biology","intvolume":"        17","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., &#38; Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>","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.","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” <i>PLoS Computational Biology</i>, vol. 17, no. 4. Public Library of Science, 2021.","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>.","chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>.","ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. 2021;17(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021)."},"type":"journal_article","volume":17,"ddc":["000"]},{"article_processing_charge":"No","title":"Defining the speciation continuum","date_created":"2021-05-09T22:01:39Z","oa_version":"Published Version","publication_status":"published","issue":"6","file_date_updated":"2022-03-25T12:02:04Z","article_type":"original","page":"1256-1273","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."}],"external_id":{"isi":["000647226400001"]},"file":[{"file_size":719991,"file_id":"10921","date_updated":"2022-03-25T12:02:04Z","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","access_level":"open_access","date_created":"2022-03-25T12:02:04Z","success":1,"content_type":"application/pdf","file_name":"2021_Evolution_Stankowski.pdf","relation":"main_file","creator":"kschuh"}],"isi":1,"publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"scopus_import":"1","oa":1,"has_accepted_license":"1","status":"public","day":"22","date_published":"2021-03-22T00:00:00Z","doi":"10.1111/evo.14215","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.","publication":"Evolution","intvolume":"        75","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Defining the speciation continuum. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. <i>Evolution</i>. 2021;75(6):1256-1273. doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021."},"volume":75,"ddc":["570"],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"03","year":"2021","date_updated":"2023-10-18T08:16:01Z","_id":"9383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"NanoFab"}],"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","full_name":"Valentini, Marco"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"oa":1,"year":"2021","contributor":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person","last_name":"Valentini"}],"date_updated":"2025-06-12T06:32:43Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"9389","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","article_processing_charge":"No","date_created":"2021-05-14T12:07:53Z","date_published":"2021-01-01T00:00:00Z","oa_version":"Published Version","related_material":{"record":[{"id":"8910","relation":"used_in_publication","status":"public"}]},"doi":"10.15479/AT:ISTA:9389","file_date_updated":"2021-05-14T11:56:48Z","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","citation":{"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, <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>","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. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>.","mla":"Valentini, Marco. <i>Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","short":"M. Valentini, (2021).","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>","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."},"ddc":["530"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","file":[{"file_size":10572981,"file_id":"9390","date_updated":"2021-05-14T11:42:23Z","checksum":"80a905c4eef24dab6fb247e81a3d67f5","date_created":"2021-05-14T11:42:23Z","access_level":"open_access","creator":"mvalenti","content_type":"application/pdf","relation":"main_file","file_name":"Notebook_Valentini.pdf"},{"date_updated":"2021-05-14T11:56:48Z","file_size":99076111,"file_id":"9391","content_type":"application/x-zip-compressed","relation":"main_file","file_name":"Experimental_data.zip","creator":"mvalenti","checksum":"1e61a7e63949448a8db0091cdac23570","access_level":"open_access","date_created":"2021-05-14T11:56:48Z"}]},{"issue":"9","article_processing_charge":"No","title":"Quantifying the use of species concepts","date_created":"2021-05-16T22:01:46Z","oa_version":"Published Version","publication_status":"published","page":"R428-R429","abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"pmid":1,"article_type":"original","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"}],"corr_author":"1","isi":1,"publisher":"Cell Press","department":[{"_id":"NiBa"}],"status":"public","scopus_import":"1","oa":1,"doi":"10.1016/j.cub.2021.03.060","day":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"date_published":"2021-05-10T00:00:00Z","citation":{"ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021."},"type":"journal_article","volume":31,"ddc":["570"],"publication":"Current Biology","acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","intvolume":"        31","quality_controlled":"1","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"date_updated":"2026-06-18T19:49:12Z","_id":"9392","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021"},{"year":"2021","date_updated":"2025-04-15T07:23:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9393","publication_identifier":{"issn":["0925-9856"],"eissn":["1572-8102"]},"ec_funded":1,"month":"09","intvolume":"        57","publication":"Formal Methods in System Design","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.","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>, vol. 57, Springer, 2021, pp. 401–28, doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. 2021;57:401-428. doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” <i>Formal Methods in System Design</i>, vol. 57. Springer, pp. 401–428, 2021.","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.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>"},"volume":57,"day":"01","date_published":"2021-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07384"}],"doi":"10.1007/s10703-021-00373-5","oa":1,"scopus_import":"1","status":"public","isi":1,"department":[{"_id":"KrCh"}],"publisher":"Springer","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"article_type":"original","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."}],"external_id":{"isi":["000645490300001"],"arxiv":["1504.07384"]},"page":"401-428","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","article_processing_charge":"No","arxiv":1,"date_created":"2021-05-16T22:01:47Z","oa_version":"Preprint","publication_status":"published"},{"date_updated":"2026-04-07T14:01:29Z","_id":"9394","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","month":"05","publication_identifier":{"eissn":["2056-3744"]},"ec_funded":1,"type":"journal_article","citation":{"ieee":"E. L. Koch <i>et al.</i>, “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” <i>Evolution Letters</i>, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. 2021;5(3):196-213. doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>","ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213."},"volume":5,"ddc":["570"],"publication":"Evolution Letters","acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","intvolume":"         5","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1002/evl3.227","day":"07","date_published":"2021-05-07T00:00:00Z","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"author":[{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"last_name":"Larsson","first_name":"Jenny","full_name":"Larsson, Jenny"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, E. Moriarty","last_name":"Lemmon","first_name":"E. Moriarty"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"project":[{"call_identifier":"H2020","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"isi":1,"publisher":"Wiley","department":[{"_id":"NiBa"}],"page":"196-213","external_id":{"isi":["000647846200001"]},"abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"file":[{"date_updated":"2021-10-15T08:26:02Z","file_size":3021108,"file_id":"10142","creator":"cchlebak","file_name":"2021_EvolutionLetters_Koch.pdf","relation":"main_file","content_type":"application/pdf","checksum":"023b1608e311f0fda30593ba3d0a4e0b","success":1,"date_created":"2021-10-15T08:26:02Z","access_level":"open_access"}],"file_date_updated":"2021-10-15T08:26:02Z","article_type":"original","issue":"3","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","article_processing_charge":"No","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"12987"}]},"oa_version":"Published Version","date_created":"2021-05-16T22:01:47Z"},{"publication_identifier":{"isbn":["978-0-262-04559-9"]},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"MIT Press","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"},{"last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"}],"month":"03","series_title":"Strüngmann Forum Reports","year":"2021","oa":1,"date_updated":"2026-06-18T19:49:35Z","_id":"9403","editor":[{"first_name":"Ralph","last_name":"Hertwig","full_name":"Hertwig, Ralph"},{"last_name":"Engel","first_name":"Christoph","full_name":"Engel, Christoph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"01","article_processing_charge":"No","title":"The evolution of strategic ignorance in strategic interaction","main_file_link":[{"url":"https://esforum.de/publications/PDFs/sfr29/SFR29_09_Hilbe%20and%20Schmid.pdf","open_access":"1"}],"date_published":"2021-03-01T00:00:00Z","oa_version":"Published Version","date_created":"2021-05-19T12:25:42Z","publication":"Deliberate Ignorance: Choosing Not To Know","intvolume":"        29","quality_controlled":"1","language":[{"iso":"eng"}],"page":"139-152","type":"book_chapter","citation":{"ieee":"L. Schmid and C. Hilbe, “The evolution of strategic ignorance in strategic interaction,” in <i>Deliberate Ignorance: Choosing Not To Know</i>, vol. 29, R. Hertwig and C. Engel, Eds. MIT Press, 2021, pp. 139–152.","chicago":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” In <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, 29:139–52. Strüngmann Forum Reports. MIT Press, 2021.","mla":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, vol. 29, MIT Press, 2021, pp. 139–52.","short":"L. Schmid, C. Hilbe, in:, R. Hertwig, C. Engel (Eds.), Deliberate Ignorance: Choosing Not To Know, MIT Press, 2021, pp. 139–152.","ama":"Schmid L, Hilbe C. The evolution of strategic ignorance in strategic interaction. In: Hertwig R, Engel C, eds. <i>Deliberate Ignorance: Choosing Not To Know</i>. Vol 29. Strüngmann Forum Reports. MIT Press; 2021:139-152.","apa":"Schmid, L., &#38; Hilbe, C. (2021). The evolution of strategic ignorance in strategic interaction. In R. Hertwig &#38; C. Engel (Eds.), <i>Deliberate Ignorance: Choosing Not To Know</i> (Vol. 29, pp. 139–152). MIT Press.","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."},"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"}],"volume":29,"ddc":["000"]},{"has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","author":[{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271"},{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"},{"full_name":"Timme, Marc","first_name":"Marc","last_name":"Timme"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"isi":1,"department":[{"_id":"BjHo"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios."}],"external_id":{"isi":["000687305500044"],"pmid":["33972522"]},"pmid":1,"file":[{"file_size":1176573,"file_id":"9426","date_updated":"2021-05-25T14:18:40Z","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","date_created":"2021-05-25T14:18:40Z","success":1,"access_level":"open_access","creator":"kschuh","file_name":"2021_NatureCommunications_Scarselli.pdf","relation":"main_file","content_type":"application/pdf"}],"article_type":"original","file_date_updated":"2021-05-25T14:18:40Z","issue":"1","article_processing_charge":"No","title":"Discontinuous epidemic transition due to limited testing","oa_version":"Published Version","date_created":"2021-05-23T22:01:42Z","publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release","description":"News on IST Homepage"}]},"date_updated":"2026-04-03T09:37:18Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9407","year":"2021","month":"05","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","citation":{"ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>","apa":"Scarselli, D., Budanur, N. B., Timme, M., &#38; Hof, B. (2021). Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586."},"ddc":["570"],"volume":12,"intvolume":"        12","publication":"Nature Communications","acknowledgement":"The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden.","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1038/s41467-021-22725-9","day":"10","article_number":"2586","date_published":"2021-05-10T00:00:00Z"},{"issue":"6","date_created":"2021-05-23T22:01:42Z","publication_status":"published","oa_version":"Published Version","title":"Computational design of skinned Quad-Robots","article_processing_charge":"No","pmid":1,"file":[{"creator":"kschuh","content_type":"application/pdf","file_name":"2021_TVCG_Feng.pdf","relation":"main_file","date_created":"2021-05-25T15:08:49Z","success":1,"access_level":"open_access","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","date_updated":"2021-05-25T15:08:49Z","file_id":"9427","file_size":6183002}],"external_id":{"isi":["000649620700009"],"pmid":["31804937"]},"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"}],"file_date_updated":"2021-05-25T15:08:49Z","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"author":[{"last_name":"Feng","first_name":"Xudong","full_name":"Feng, Xudong"},{"full_name":"Liu, Jiafeng","first_name":"Jiafeng","last_name":"Liu"},{"first_name":"Huamin","last_name":"Wang","full_name":"Wang, Huamin"},{"full_name":"Yang, Yin","last_name":"Yang","first_name":"Yin"},{"full_name":"Bao, Hujun","last_name":"Bao","first_name":"Hujun"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"department":[{"_id":"BeBi"}],"publisher":"IEEE","isi":1,"has_accepted_license":"1","status":"public","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1109/TVCG.2019.2957218","date_published":"2021-06-01T00:00:00Z","article_number":"2881-2895","day":"01","ddc":["000"],"volume":27,"type":"journal_article","citation":{"apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., &#38; Xu, W. (2021). Computational design of skinned Quad-Robots. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">https://doi.org/10.1109/TVCG.2019.2957218</a>","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.","ieee":"X. Feng <i>et al.</i>, “Computational design of skinned Quad-Robots,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 27, no. 6. IEEE, 2021.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">https://doi.org/10.1109/TVCG.2019.2957218</a>.","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:<a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">10.1109/TVCG.2019.2957218</a>.","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2021;27(6). doi:<a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">10.1109/TVCG.2019.2957218</a>","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021)."},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        27","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":"IEEE Transactions on Visualization and Computer Graphics","month":"06","ec_funded":1,"publication_identifier":{"issn":["1941-0506"],"eissn":["1077-2626"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9408","date_updated":"2025-07-10T12:01:44Z","year":"2021"},{"publisher":"Royal Society of London","department":[{"_id":"NiBa"}],"isi":1,"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","last_name":"Uecker"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","oa_version":"Published Version","publication_status":"published","date_created":"2021-05-23T22:01:43Z","title":"Adaptation at different points along antibiotic concentration gradients","article_processing_charge":"No","issue":"5","file_date_updated":"2021-05-25T14:09:03Z","pmid":1,"file":[{"date_updated":"2021-05-25T14:09:03Z","file_id":"9425","file_size":726759,"creator":"kschuh","file_name":"2021_BiologyLetters_Lagator.pdf","content_type":"application/pdf","relation":"main_file","success":1,"date_created":"2021-05-25T14:09:03Z","access_level":"open_access","checksum":"9c13c1f5af7609c97c741f11d293188a"}],"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"abstract":[{"lang":"eng","text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains."}],"ec_funded":1,"publication_identifier":{"eissn":["1744-957X"]},"month":"05","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9410","date_updated":"2026-04-02T14:02:44Z","date_published":"2021-05-12T00:00:00Z","article_number":"20200913","day":"12","doi":"10.1098/rsbl.2020.0913","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        17","publication":"Biology letters","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","ddc":["570"],"volume":17,"citation":{"ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” <i>Biology letters</i>, vol. 17, no. 5. Royal Society of London, 2021.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. <i>Biology letters</i>. 2021;17(5). doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>. Royal Society of London, 2021. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>.","apa":"Lagator, M., Uecker, H., &#38; Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913."},"type":"journal_article"},{"file_date_updated":"2021-05-25T11:32:14Z","external_id":{"isi":["000643251300001"]},"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"}],"file":[{"file_size":2507870,"file_id":"9422","date_updated":"2021-05-25T11:32:14Z","checksum":"0ef342d011afbe3c5cb058fda9a3f395","access_level":"open_access","date_created":"2021-05-25T11:32:14Z","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2021_EPJE_Sukhov.pdf","creator":"kschuh"}],"article_processing_charge":"No","title":"Regimes of motion of magnetocapillary swimmers","publication_status":"published","oa_version":"Published Version","date_created":"2021-05-23T22:01:44Z","issue":"4","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"status":"public","has_accepted_license":"1","isi":1,"department":[{"_id":"ScWa"}],"publisher":"Springer","author":[{"full_name":"Sukhov, Alexander","last_name":"Sukhov","first_name":"Alexander"},{"last_name":"Hubert","first_name":"Maxime","full_name":"Hubert, Maxime"},{"full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","last_name":"Grosjean"},{"last_name":"Trosman","first_name":"Oleg","full_name":"Trosman, Oleg"},{"last_name":"Ziegler","first_name":"Sebastian","full_name":"Ziegler, Sebastian"},{"full_name":"Collard, Ylona","first_name":"Ylona","last_name":"Collard"},{"first_name":"Nicolas","last_name":"Vandewalle","full_name":"Vandewalle, Nicolas"},{"last_name":"Smith","first_name":"Ana Sunčana","full_name":"Smith, Ana Sunčana"},{"first_name":"Jens","last_name":"Harting","full_name":"Harting, Jens"}],"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":"European Physical Journal E","intvolume":"        44","quality_controlled":"1","language":[{"iso":"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).","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. <i>European Physical Journal E</i>. 2021;44(4). doi:<a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">10.1140/epje/s10189-021-00065-2</a>","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.” <i>European Physical Journal E</i>. Springer, 2021. <a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">https://doi.org/10.1140/epje/s10189-021-00065-2</a>.","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” <i>European Physical Journal E</i>, vol. 44, no. 4, 59, Springer, 2021, doi:<a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">10.1140/epje/s10189-021-00065-2</a>.","ieee":"A. Sukhov <i>et al.</i>, “Regimes of motion of magnetocapillary swimmers,” <i>European Physical Journal E</i>, vol. 44, no. 4. Springer, 2021.","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.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. <i>European Physical Journal E</i>. Springer. <a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">https://doi.org/10.1140/epje/s10189-021-00065-2</a>"},"type":"journal_article","volume":44,"ddc":["530"],"day":"24","article_number":"59","date_published":"2021-04-24T00:00:00Z","doi":"10.1140/epje/s10189-021-00065-2","year":"2021","date_updated":"2025-07-10T12:01:45Z","_id":"9411","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"month":"04"},{"year":"2021","date_updated":"2026-04-02T14:00:37Z","_id":"9412","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1083-6489"]},"ec_funded":1,"month":"03","publication":"Electronic Journal of Probability","intvolume":"        26","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>"},"type":"journal_article","volume":26,"ddc":["510"],"day":"23","article_number":"24","date_published":"2021-03-23T00:00:00Z","doi":"10.1214/21-EJP591","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"has_accepted_license":"1","status":"public","isi":1,"department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","author":[{"last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"file_date_updated":"2021-05-25T13:24:19Z","external_id":{"isi":["000641855600001"],"arxiv":["2002.02438"]},"abstract":[{"text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness.","lang":"eng"}],"file":[{"date_updated":"2021-05-25T13:24:19Z","file_id":"9423","file_size":865148,"creator":"kschuh","file_name":"2021_EJP_Cipolloni.pdf","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2021-05-25T13:24:19Z","access_level":"open_access","checksum":"864ab003ad4cffea783f65aa8c2ba69f"}],"arxiv":1,"title":"Fluctuation around the circular law for random matrices with real entries","article_processing_charge":"No","publication_status":"published","date_created":"2021-05-23T22:01:44Z","oa_version":"Published Version"},{"article_type":"original","page":"869-879","external_id":{"isi":["000641574700005"],"pmid":["33439671"]},"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"}],"pmid":1,"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","title":"Spatial variation of microtubule depolymerization in large asters","article_processing_charge":"No","publication_status":"published","date_created":"2021-05-23T22:01:45Z","oa_version":"Published Version","issue":"9","tmp":{"short":"CC BY-NC-SA (3.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode"},"scopus_import":"1","oa":1,"status":"public","isi":1,"department":[{"_id":"MaLo"}],"publisher":"American Society for Cell Biology","author":[{"full_name":"Ishihara, Keisuke","last_name":"Ishihara","first_name":"Keisuke"},{"last_name":"Decker","first_name":"Franziska","full_name":"Decker, Franziska"},{"orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas"},{"full_name":"Pelletier, James F.","last_name":"Pelletier","first_name":"James F."},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"last_name":"Mitchison","first_name":"Timothy J.","full_name":"Mitchison, Timothy J."}],"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"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.","publication":"Molecular Biology of the Cell","intvolume":"        32","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"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.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2021. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>.","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>.","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.","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. 2021;32(9):869-879. doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>","ieee":"K. Ishihara <i>et al.</i>, “Spatial variation of microtubule depolymerization in large asters,” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","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., &#38; Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>"},"volume":32,"ddc":["570"],"day":"19","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"date_published":"2021-04-19T00:00:00Z","doi":"10.1091/MBC.E20-11-0723","year":"2021","date_updated":"2026-06-18T19:52:16Z","_id":"9414","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"ec_funded":1,"month":"04"},{"doi":"10.1038/s41467-021-23506-0","day":"28","article_number":"3226","date_published":"2021-05-28T00:00:00Z","citation":{"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).","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. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","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.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","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.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","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.","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. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>"},"type":"journal_article","ddc":["570"],"volume":12,"intvolume":"        12","publication":"Nature Communications","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).","language":[{"iso":"eng"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"month":"05","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2025-04-15T08:24:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9431","year":"2021","issue":"1","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","article_processing_charge":"No","publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"oa_version":"Published Version","date_created":"2021-05-28T14:25:50Z","abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000659145000011"]},"file":[{"creator":"kschuh","relation":"main_file","file_name":"2021_NatureCommunications_Obr.pdf","content_type":"application/pdf","success":1,"date_created":"2021-06-09T15:21:14Z","access_level":"open_access","checksum":"53ccc53d09a9111143839dbe7784e663","date_updated":"2021-06-09T15:21:14Z","file_id":"9538","file_size":6166295}],"article_type":"original","file_date_updated":"2021-06-09T15:21:14Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Nikulin, Nadia","first_name":"Nadia","last_name":"Nikulin"},{"full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R.","last_name":"Feathers"},{"full_name":"Klanschnig, Marco","first_name":"Marco","last_name":"Klanschnig"},{"full_name":"Thader, Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"}],"corr_author":"1","isi":1,"department":[{"_id":"FlSc"}],"publisher":"Nature Research","status":"public","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1"},{"department":[{"_id":"VaKa"}],"corr_author":"1","author":[{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"last_name":"Koudjinan","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","first_name":"Edmond","full_name":"Koudjinan, Edmond","orcid":"0000-0003-2640-4049"}],"oa":1,"has_accepted_license":"1","status":"public","oa_version":"Submitted Version","date_created":"2021-05-30T13:58:13Z","publication_status":"submitted","article_processing_charge":"No","title":"Non co-preservation of the 1/2 and  1/(2l+1)-rational caustics along deformations of circles","arxiv":1,"file_date_updated":"2021-05-30T13:57:37Z","file":[{"date_updated":"2021-05-30T13:57:37Z","file_size":353431,"file_id":"9436","relation":"main_file","content_type":"application/pdf","file_name":"CoExistence 2&3 caustics 3_17_6_2_3.pdf","creator":"ekoudjin","checksum":"b281b5c2e3e90de0646c3eafcb2c6c25","access_level":"open_access","date_created":"2021-05-30T13:57:37Z"}],"abstract":[{"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).","lang":"eng"}],"external_id":{"arxiv":["2107.03499"]},"month":"07","year":"2021","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9435","date_updated":"2025-01-22T08:09:40Z","article_number":"2107.03499","date_published":"2021-07-07T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.03499","open_access":"1"}],"day":"07","doi":"10.48550/arXiv.2107.03499","language":[{"iso":"eng"}],"publication":"arXiv","ddc":["500"],"citation":{"apa":"Kaloshin, V., &#38; Koudjinan, E. (n.d.). Non co-preservation of the 1/2 and  1/(2l+1)-rational caustics along deformations of circles. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2107.03499\">https://doi.org/10.48550/arXiv.2107.03499</a>","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.","ieee":"V. Kaloshin and E. Koudjinan, “Non co-preservation of the 1/2 and  1/(2l+1)-rational caustics along deformations of circles,” <i>arXiv</i>. .","short":"V. Kaloshin, E. Koudjinan, ArXiv (n.d.).","ama":"Kaloshin V, Koudjinan E. Non co-preservation of the 1/2 and  1/(2l+1)-rational caustics along deformations of circles. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2107.03499\">10.48550/arXiv.2107.03499</a>","mla":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and  1/(2l+1)-Rational Caustics along Deformations of Circles.” <i>ArXiv</i>, 2107.03499, doi:<a href=\"https://doi.org/10.48550/arXiv.2107.03499\">10.48550/arXiv.2107.03499</a>.","chicago":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and  1/(2l+1)-Rational Caustics along Deformations of Circles.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2107.03499\">https://doi.org/10.48550/arXiv.2107.03499</a>."},"type":"preprint"},{"day":"20","main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"date_published":"2021-05-20T00:00:00Z","doi":"10.1038/s41593-021-00846-0","publication":"Nature Neuroscience","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.","intvolume":"        24","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","apa":"Mlynarski, W. F., &#38; Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00846-0\">https://doi.org/10.1038/s41593-021-00846-0</a>","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. <i>Nature Neuroscience</i>. 2021;24:998-1009. doi:<a href=\"https://doi.org/10.1038/s41593-021-00846-0\">10.1038/s41593-021-00846-0</a>","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.” <i>Nature Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00846-0\">https://doi.org/10.1038/s41593-021-00846-0</a>.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” <i>Nature Neuroscience</i>, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:<a href=\"https://doi.org/10.1038/s41593-021-00846-0\">10.1038/s41593-021-00846-0</a>.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” <i>Nature Neuroscience</i>, vol. 24. Springer Nature, pp. 998–1009, 2021."},"type":"journal_article","volume":24,"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"ec_funded":1,"month":"05","year":"2021","date_updated":"2025-06-12T06:41:38Z","_id":"9439","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Efficient and adaptive sensory codes","date_created":"2021-05-30T22:01:24Z","oa_version":"Preprint","publication_status":"published","article_type":"original","page":"998-1009","external_id":{"isi":["000652577300003"],"pmid":["34017131"]},"abstract":[{"lang":"eng","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."}],"pmid":1,"isi":1,"department":[{"_id":"GaTk"}],"publisher":"Springer Nature","author":[{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"full_name":"Hermundstad, Ann M.","last_name":"Hermundstad","first_name":"Ann M."}],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","oa":1,"status":"public"},{"year":"2021","date_updated":"2025-04-14T07:45:00Z","_id":"9443","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"ec_funded":1,"month":"07","publication":"Plant Cell","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","intvolume":"        33","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"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.","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. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab122\">https://doi.org/10.1093/plcell/koab122</a>","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.","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. <i>Plant Cell</i>. 2021;33(7):2431-2453. doi:<a href=\"https://doi.org/10.1093/plcell/koab122\">10.1093/plcell/koab122</a>","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” <i>Plant Cell</i>, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:<a href=\"https://doi.org/10.1093/plcell/koab122\">10.1093/plcell/koab122</a>.","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.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab122\">https://doi.org/10.1093/plcell/koab122</a>.","ieee":"N. Ruiz-Lopez <i>et al.</i>, “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” <i>Plant Cell</i>, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021."},"volume":33,"ddc":["580"],"day":"01","date_published":"2021-07-01T00:00:00Z","doi":"10.1093/plcell/koab122","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"scopus_import":"1","oa":1,"status":"public","has_accepted_license":"1","isi":1,"department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","author":[{"first_name":"N","last_name":"Ruiz-Lopez","full_name":"Ruiz-Lopez, N"},{"full_name":"Pérez-Sancho, J","last_name":"Pérez-Sancho","first_name":"J"},{"last_name":"Esteban Del Valle","first_name":"A","full_name":"Esteban Del Valle, A"},{"full_name":"Haslam, RP","last_name":"Haslam","first_name":"RP"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"full_name":"Catalá, R","last_name":"Catalá","first_name":"R"},{"full_name":"Perea-Resa, C","last_name":"Perea-Resa","first_name":"C"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"full_name":"García-Hernández, S","first_name":"S","last_name":"García-Hernández"},{"full_name":"Albert, A","last_name":"Albert","first_name":"A"},{"last_name":"Vallarino","first_name":"J","full_name":"Vallarino, J"},{"full_name":"Lin, J","first_name":"J","last_name":"Lin"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Macho, AP","first_name":"AP","last_name":"Macho"},{"full_name":"Salinas, J","last_name":"Salinas","first_name":"J"},{"first_name":"A","last_name":"Rosado","full_name":"Rosado, A"},{"full_name":"Napier, JA","last_name":"Napier","first_name":"JA"},{"last_name":"Amorim-Silva","first_name":"V","full_name":"Amorim-Silva, V"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"}],"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2021-10-14T13:36:38Z","article_type":"original","page":"2431-2453","external_id":{"pmid":["33944955"],"isi":["000703938100026"]},"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."}],"file":[{"success":1,"date_created":"2021-10-14T13:36:38Z","access_level":"open_access","checksum":"22d596678d00310d793611864a6d0fcd","creator":"cchlebak","relation":"main_file","file_name":"2021_PlantCell_RuizLopez.pdf","content_type":"application/pdf","file_id":"10141","file_size":2952028,"date_updated":"2021-10-14T13:36:38Z"}],"pmid":1,"article_processing_charge":"No","title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","publication_status":"published","oa_version":"Published Version","date_created":"2021-06-02T13:13:58Z","issue":"7"},{"publication_identifier":{"eissn":["1945-7111"],"issn":["0013-4651"]},"month":"05","year":"2021","_id":"9447","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-10-21T06:02:10Z","article_number":"050550","date_published":"2021-05-01T00:00:00Z","day":"01","doi":"10.1149/1945-7111/ac0300","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Journal of The Electrochemical Society","intvolume":"       168","volume":168,"type":"journal_article","citation":{"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.","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. <i>Journal of The Electrochemical Society</i>. IOP Publishing. <a href=\"https://doi.org/10.1149/1945-7111/ac0300\">https://doi.org/10.1149/1945-7111/ac0300</a>","ama":"Maffre M, Bouchal R, Freunberger SA, et al. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. <i>Journal of The Electrochemical Society</i>. 2021;168(5). doi:<a href=\"https://doi.org/10.1149/1945-7111/ac0300\">10.1149/1945-7111/ac0300</a>","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).","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.” <i>Journal of The Electrochemical Society</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1149/1945-7111/ac0300\">https://doi.org/10.1149/1945-7111/ac0300</a>.","mla":"Maffre, Marion, et al. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” <i>Journal of The Electrochemical Society</i>, vol. 168, no. 5, 050550, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1149/1945-7111/ac0300\">10.1149/1945-7111/ac0300</a>.","ieee":"M. Maffre <i>et al.</i>, “Investigation of electrochemical and chemical processes occurring at positive potentials in ‘Water-in-Salt’ electrolytes,” <i>Journal of The Electrochemical Society</i>, vol. 168, no. 5. IOP Publishing, 2021."},"department":[{"_id":"StFr"}],"publisher":"IOP Publishing","isi":1,"author":[{"first_name":"Marion","last_name":"Maffre","full_name":"Maffre, Marion"},{"last_name":"Bouchal","first_name":"Roza","full_name":"Bouchal, Roza"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger"},{"full_name":"Lindahl, Niklas","first_name":"Niklas","last_name":"Lindahl"},{"full_name":"Johansson, Patrik","last_name":"Johansson","first_name":"Patrik"},{"full_name":"Favier, Frédéric","first_name":"Frédéric","last_name":"Favier"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"full_name":"Bélanger, Daniel","first_name":"Daniel","last_name":"Bélanger"}],"scopus_import":"1","status":"public","publication_status":"published","oa_version":"None","date_created":"2021-06-03T09:58:38Z","title":"Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes","article_processing_charge":"No","issue":"5","keyword":["Renewable Energy","Sustainability and the Environment","Electrochemistry","Materials Chemistry","Electronic","Optical and Magnetic Materials","Surfaces","Coatings and Films","Condensed Matter Physics"],"external_id":{"isi":["000657724200001"]},"abstract":[{"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.","lang":"eng"}]},{"title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","article_processing_charge":"No","arxiv":1,"date_created":"2021-06-06T22:01:28Z","oa_version":"Preprint","publication_status":"published","issue":"6","article_type":"original","external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"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"}],"isi":1,"publisher":"Elsevier","department":[{"_id":"RoSe"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"oa":1,"scopus_import":"1","status":"public","day":"15","article_number":"109096","date_published":"2021-09-15T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/2009.00992","open_access":"1"}],"doi":"10.1016/j.jfa.2021.109096","intvolume":"       281","publication":"Journal of Functional Analysis","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.","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"apa":"Deuchert, A., &#38; Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109096\">https://doi.org/10.1016/j.jfa.2021.109096</a>","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” <i>Journal of Functional Analysis</i>, vol. 281, no. 6. Elsevier, 2021.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. <i>Journal of Functional Analysis</i>. 2021;281(6). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109096\">10.1016/j.jfa.2021.109096</a>","chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109096\">https://doi.org/10.1016/j.jfa.2021.109096</a>.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” <i>Journal of Functional Analysis</i>, vol. 281, no. 6, 109096, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109096\">10.1016/j.jfa.2021.109096</a>."},"type":"journal_article","volume":281,"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"ec_funded":1,"month":"09","year":"2021","date_updated":"2025-04-14T07:26:53Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9462"}]