[{"date_updated":"2023-08-08T13:33:09Z","date_created":"2021-05-07T17:10:21Z","volume":118,"author":[{"full_name":"Meier, Joana I.","first_name":"Joana I.","last_name":"Meier"},{"last_name":"Salazar","first_name":"Patricio A.","full_name":"Salazar, Patricio A."},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"first_name":"Robert William","last_name":"Davies","full_name":"Davies, Robert William"},{"first_name":"Andreea","last_name":"Dréau","full_name":"Dréau, Andreea"},{"last_name":"Aldás","first_name":"Ismael","full_name":"Aldás, Ismael"},{"last_name":"Power","first_name":"Olivia Box","full_name":"Power, Olivia Box"},{"last_name":"Nadeau","first_name":"Nicola J.","full_name":"Nadeau, Nicola J."},{"full_name":"Bridle, Jon R.","last_name":"Bridle","first_name":"Jon R."},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"McMillan, W. Owen","last_name":"McMillan","first_name":"W. Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Proceedings of the National Academy of Sciences","year":"2021","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2022-03-08T08:18:16Z","article_number":"e2015005118","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2015005118","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"month":"06","publication_identifier":{"eissn":["0027-8424"]},"oa_version":"Published Version","file":[{"checksum":"cb30c6166b2132ee60d616b31a1a7c29","success":1,"date_created":"2022-03-08T08:18:16Z","date_updated":"2022-03-08T08:18:16Z","relation":"main_file","file_id":"10835","content_type":"application/pdf","file_size":20592929,"creator":"dernst","access_level":"open_access","file_name":"2021_PNAS_Meier.pdf"}],"ddc":["570"],"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","status":"public","intvolume":" 118","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9375","abstract":[{"text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.","lang":"eng"}],"issue":"25","type":"journal_article","date_published":"2021-06-21T00:00:00Z","article_type":"original","publication":"PNAS","citation":{"ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118","chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021)."},"day":"21","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"file":[{"checksum":"023b1608e311f0fda30593ba3d0a4e0b","success":1,"date_updated":"2021-10-15T08:26:02Z","date_created":"2021-10-15T08:26:02Z","relation":"main_file","file_id":"10142","content_type":"application/pdf","file_size":3021108,"creator":"cchlebak","access_level":"open_access","file_name":"2021_EvolutionLetters_Koch.pdf"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9394","abstract":[{"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.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2021-05-07T00:00:00Z","article_type":"original","page":"196-213","publication":"Evolution Letters","citation":{"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. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","ieee":"E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","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.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227","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.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.","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.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227."},"day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-08T13:34:08Z","date_created":"2021-05-16T22:01:47Z","volume":5,"author":[{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty","last_name":"Lemmon"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"12987"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2021","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. ","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2021-10-15T08:26:02Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1002/evl3.227","isi":1,"quality_controlled":"1","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000647846200001"]},"oa":1,"month":"05","publication_identifier":{"eissn":["2056-3744"]}},{"date_published":"2021-04-01T00:00:00Z","article_type":"original","citation":{"ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4). doi:10.1371/journal.pcbi.1008523","apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology, vol. 17, no. 4. Public Library of Science, 2021.","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.","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021).","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008523.","chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523."},"publication":"PLoS Computational Biology","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9385","date_updated":"2021-05-11T13:50:06Z","date_created":"2021-05-11T13:50:06Z","checksum":"a94ebe0c4116f5047eaa6029e54d2dac","success":1,"file_name":"2021_pcbi_Kleshnina.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1323820,"creator":"kschuh"}],"intvolume":" 17","title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","ddc":["000"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9381","issue":"4","abstract":[{"lang":"eng","text":"A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1008523","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000639711200001"]},"publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"month":"04","volume":17,"date_created":"2021-05-09T22:01:38Z","date_updated":"2023-08-08T13:31:08Z","author":[{"full_name":"Kleshnina, Maria","first_name":"Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Streipert","first_name":"Sabrina S.","full_name":"Streipert, Sabrina S."},{"last_name":"Filar","first_name":"Jerzy A.","full_name":"Filar, Jerzy A."},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","year":"2021","ec_funded":1,"file_date_updated":"2021-05-11T13:50:06Z","article_number":"e1008523"},{"scopus_import":"1","article_processing_charge":"No","day":"10","page":"R428-R429","article_type":"original","citation":{"short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429."},"publication":"Current Biology","date_published":"2021-05-10T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"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.","lang":"eng"}],"intvolume":" 31","title":"Quantifying the use of species concepts","status":"public","_id":"9392","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","publication_identifier":{"issn":["09609822"],"eissn":["18790445"]},"month":"05","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"oa":1,"external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2021.03.060","publisher":"Cell Press","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"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.","year":"2021","volume":31,"date_updated":"2023-08-08T13:34:38Z","date_created":"2021-05-16T22:01:46Z","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}]},{"article_number":"110729","author":[{"full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","last_name":"Khudiakova"},{"full_name":"Neretina, Tatiana Yu.","first_name":"Tatiana Yu.","last_name":"Neretina"},{"first_name":"Alexey S.","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S."}],"date_updated":"2023-08-08T13:32:40Z","date_created":"2021-05-12T05:58:42Z","volume":524,"year":"2021","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","publication_status":"published","publisher":"Elsevier ","department":[{"_id":"GradSch"}],"month":"04","publication_identifier":{"issn":["0022-5193"]},"doi":"10.1016/j.jtbi.2021.110729","language":[{"iso":"eng"}],"external_id":{"isi":["000659161500002"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/477489v1","open_access":"1"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift."}],"type":"journal_article","oa_version":"Preprint","_id":"9387","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","intvolume":" 524","day":"24","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"date_published":"2021-04-24T00:00:00Z","publication":"Journal of Theoretical Biology","citation":{"ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021.","apa":"Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.","chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729."},"article_type":"original"},{"has_accepted_license":"1","article_processing_charge":"No","day":"10","month":"04","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"oa":1,"citation":{"apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4."},"doi":"10.5061/DRYAD.ZGMSBCCB4","date_published":"2021-04-10T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"12987","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","status":"public","ddc":["570"],"related_material":{"record":[{"id":"9394","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Koch","first_name":"Eva","full_name":"Koch, Eva"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty","last_name":"Lemmon"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"oa_version":"Published Version","date_created":"2023-05-16T12:34:09Z","date_updated":"2023-08-08T13:34:07Z"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-06-01T00:00:00Z","publication":"IEEE Transactions on Visualization and Computer Graphics","citation":{"ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","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 et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218.","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218."},"abstract":[{"lang":"eng","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."}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"9427","date_updated":"2021-05-25T15:08:49Z","date_created":"2021-05-25T15:08:49Z","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","success":1,"file_name":"2021_TVCG_Feng.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6183002,"creator":"kschuh"}],"oa_version":"Published Version","ddc":["000"],"status":"public","title":"Computational design of skinned Quad-Robots","intvolume":" 27","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9408","month":"06","publication_identifier":{"eissn":["10772626"],"issn":["19410506"]},"language":[{"iso":"eng"}],"doi":"10.1109/TVCG.2019.2957218","quality_controlled":"1","isi":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000649620700009"],"pmid":["31804937"]},"file_date_updated":"2021-05-25T15:08:49Z","ec_funded":1,"article_number":"2881-2895","date_updated":"2023-08-08T13:45:46Z","date_created":"2021-05-23T22:01:42Z","volume":27,"author":[{"first_name":"Xudong","last_name":"Feng","full_name":"Feng, Xudong"},{"first_name":"Jiafeng","last_name":"Liu","full_name":"Liu, Jiafeng"},{"full_name":"Wang, Huamin","first_name":"Huamin","last_name":"Wang"},{"last_name":"Yang","first_name":"Yin","full_name":"Yang, Yin"},{"last_name":"Bao","first_name":"Hujun","full_name":"Bao, Hujun"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"BeBi"}],"year":"2021","acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","pmid":1},{"_id":"9410","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Adaptation at different points along antibiotic concentration gradients","status":"public","intvolume":" 17","file":[{"checksum":"9c13c1f5af7609c97c741f11d293188a","success":1,"date_updated":"2021-05-25T14:09:03Z","date_created":"2021-05-25T14:09:03Z","relation":"main_file","file_id":"9425","file_size":726759,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2021_BiologyLetters_Lagator.pdf"}],"oa_version":"Published Version","type":"journal_article","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."}],"issue":"5","publication":"Biology letters","citation":{"ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913."},"date_published":"2021-05-12T00:00:00Z","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","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.","year":"2021","pmid":1,"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"NiBa"}],"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","last_name":"Uecker"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"date_created":"2021-05-23T22:01:43Z","date_updated":"2023-08-08T13:44:35Z","volume":17,"article_number":"20200913","file_date_updated":"2021-05-25T14:09:03Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"doi":"10.1098/rsbl.2020.0913","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1744957X"]}},{"author":[{"first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"}],"date_updated":"2023-08-08T13:39:19Z","date_created":"2021-05-23T22:01:44Z","volume":26,"year":"2021","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","file_date_updated":"2021-05-25T13:24:19Z","ec_funded":1,"article_number":"24","doi":"10.1214/21-EJP591","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"03","publication_identifier":{"eissn":["10836489"]},"file":[{"date_created":"2021-05-25T13:24:19Z","date_updated":"2021-05-25T13:24:19Z","checksum":"864ab003ad4cffea783f65aa8c2ba69f","success":1,"relation":"main_file","file_id":"9423","file_size":865148,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_EJP_Cipolloni.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9412","ddc":["510"],"title":"Fluctuation around the circular law for random matrices with real entries","status":"public","intvolume":" 26","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2021-03-23T00:00:00Z","publication":"Electronic Journal of Probability","citation":{"apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, 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.","ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591."},"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9.","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586."},"article_type":"original","date_published":"2021-05-10T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1","_id":"9407","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Discontinuous epidemic transition due to limited testing","ddc":["570"],"status":"public","intvolume":" 12","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_NatureCommunications_Scarselli.pdf","file_size":1176573,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"9426","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","success":1,"date_created":"2021-05-25T14:18:40Z","date_updated":"2021-05-25T14:18:40Z"}],"month":"05","publication_identifier":{"eissn":["20411723"]},"external_id":{"isi":["000687305500044"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-22725-9","language":[{"iso":"eng"}],"article_number":"2586","file_date_updated":"2021-05-25T14:18:40Z","year":"2021","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.","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","author":[{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B"},{"first_name":"Marc","last_name":"Timme","full_name":"Timme, Marc"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2021-05-23T22:01:42Z","date_updated":"2023-08-08T13:45:13Z","volume":12},{"publication_identifier":{"eissn":["1292895X"],"issn":["12928941"]},"month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000643251300001"]},"quality_controlled":"1","isi":1,"doi":"10.1140/epje/s10189-021-00065-2","language":[{"iso":"eng"}],"article_number":"59","file_date_updated":"2021-05-25T11:32:14Z","year":"2021","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.","publisher":"Springer","department":[{"_id":"ScWa"}],"publication_status":"published","author":[{"first_name":"Alexander","last_name":"Sukhov","full_name":"Sukhov, Alexander"},{"last_name":"Hubert","first_name":"Maxime","full_name":"Hubert, Maxime"},{"last_name":"Grosjean","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M"},{"first_name":"Oleg","last_name":"Trosman","full_name":"Trosman, Oleg"},{"first_name":"Sebastian","last_name":"Ziegler","full_name":"Ziegler, Sebastian"},{"full_name":"Collard, Ylona","first_name":"Ylona","last_name":"Collard"},{"full_name":"Vandewalle, Nicolas","first_name":"Nicolas","last_name":"Vandewalle"},{"full_name":"Smith, Ana Sunčana","first_name":"Ana Sunčana","last_name":"Smith"},{"full_name":"Harting, Jens","last_name":"Harting","first_name":"Jens"}],"volume":44,"date_updated":"2023-08-08T13:36:28Z","date_created":"2021-05-23T22:01:44Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2.","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).","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.","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2"},"publication":"European Physical Journal E","date_published":"2021-04-24T00:00:00Z","type":"journal_article","issue":"4","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"}],"_id":"9411","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 44","ddc":["530"],"status":"public","title":"Regimes of motion of magnetocapillary swimmers","file":[{"success":1,"checksum":"0ef342d011afbe3c5cb058fda9a3f395","date_updated":"2021-05-25T11:32:14Z","date_created":"2021-05-25T11:32:14Z","file_id":"9422","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":2507870,"access_level":"open_access","file_name":"2021_EPJE_Sukhov.pdf"}],"oa_version":"Published Version"},{"type":"journal_article","issue":"9","abstract":[{"lang":"eng","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."}],"intvolume":" 32","status":"public","title":"Spatial variation of microtubule depolymerization in large asters","_id":"9414","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"19","page":"869-879","article_type":"original","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.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.","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.","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.","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723"},"publication":"Molecular Biology of the Cell","date_published":"2021-04-19T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","ec_funded":1,"department":[{"_id":"MaLo"}],"publisher":"American Society for Cell Biology","publication_status":"published","year":"2021","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","volume":32,"date_updated":"2023-08-08T13:36:02Z","date_created":"2021-05-23T22:01:45Z","author":[{"full_name":"Ishihara, Keisuke","first_name":"Keisuke","last_name":"Ishihara"},{"first_name":"Franziska","last_name":"Decker","full_name":"Decker, Franziska"},{"orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R"},{"first_name":"James F.","last_name":"Pelletier","full_name":"Pelletier, James F."},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"},{"first_name":"Jan","last_name":"Brugués","full_name":"Brugués, Jan"},{"last_name":"Mitchison","first_name":"Timothy J.","full_name":"Mitchison, Timothy J."}],"publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"month":"04","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000641574700005"]},"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"},"main_file_link":[{"url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1091/MBC.E20-11-0723"},{"abstract":[{"lang":"eng","text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision."}],"type":"conference","oa_version":"Published Version","file":[{"date_created":"2021-06-16T08:23:54Z","date_updated":"2021-06-16T08:23:54Z","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","success":1,"relation":"main_file","file_id":"9557","content_type":"application/pdf","file_size":641990,"creator":"esarac","file_name":"qam.pdf","access_level":"open_access"}],"title":"Quantitative and approximate monitoring","ddc":["000"],"status":"public","_id":"9356","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2021-06-29T00:00:00Z","citation":{"ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547","apa":"Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547."},"publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","file_date_updated":"2021-06-16T08:23:54Z","article_number":"9470547","date_created":"2021-04-30T17:30:47Z","date_updated":"2023-08-08T13:52:56Z","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","year":"2021","month":"06","language":[{"iso":"eng"}],"doi":"10.1109/LICS52264.2021.9470547","conference":{"name":"LICS: Symposium on Logic in Computer Science","location":"Online","start_date":"2021-06-29","end_date":"2021-07-02"},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000947350400021"],"arxiv":["2105.08353"]}},{"ec_funded":1,"year":"2021","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","publisher":"Springer Nature","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ann M.","last_name":"Hermundstad","full_name":"Hermundstad, Ann M."}],"volume":24,"date_updated":"2023-08-08T13:51:14Z","date_created":"2021-05-30T22:01:24Z","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/669200 "}],"external_id":{"isi":["000652577300003"]},"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41593-021-00846-0","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9439","intvolume":" 24","status":"public","title":"Efficient and adaptive sensory codes","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"20","citation":{"chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0"},"publication":"Nature Neuroscience","page":"998-1009","article_type":"original","date_published":"2021-05-20T00:00:00Z"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-07-01T00:00:00Z","publication":"Plant Cell","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. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","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."},"article_type":"original","page":"2431-2453","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."}],"issue":"7","type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":2952028,"file_name":"2021_PlantCell_RuizLopez.pdf","access_level":"open_access","date_created":"2021-10-14T13:36:38Z","date_updated":"2021-10-14T13:36:38Z","success":1,"checksum":"22d596678d00310d793611864a6d0fcd","file_id":"10141","relation":"main_file"}],"_id":"9443","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580"],"title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","status":"public","intvolume":" 33","month":"07","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"doi":"10.1093/plcell/koab122","language":[{"iso":"eng"}],"external_id":{"pmid":["33944955"],"isi":["000703938100026"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"file_date_updated":"2021-10-14T13:36:38Z","ec_funded":1,"author":[{"last_name":"Ruiz-Lopez","first_name":"N","full_name":"Ruiz-Lopez, N"},{"first_name":"J","last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, J"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"last_name":"Haslam","first_name":"RP","full_name":"Haslam, RP"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"full_name":"Catalá, R","first_name":"R","last_name":"Catalá"},{"first_name":"C","last_name":"Perea-Resa","full_name":"Perea-Resa, C"},{"last_name":"Van Damme","first_name":"D","full_name":"Van Damme, D"},{"full_name":"García-Hernández, S","last_name":"García-Hernández","first_name":"S"},{"full_name":"Albert, A","last_name":"Albert","first_name":"A"},{"first_name":"J","last_name":"Vallarino","full_name":"Vallarino, J"},{"full_name":"Lin, J","last_name":"Lin","first_name":"J"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"AP","last_name":"Macho","full_name":"Macho, AP"},{"full_name":"Salinas, J","first_name":"J","last_name":"Salinas"},{"full_name":"Rosado, A","first_name":"A","last_name":"Rosado"},{"last_name":"Napier","first_name":"JA","full_name":"Napier, JA"},{"last_name":"Amorim-Silva","first_name":"V","full_name":"Amorim-Silva, V"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"}],"date_created":"2021-06-02T13:13:58Z","date_updated":"2023-08-08T13:54:32Z","volume":33,"year":"2021","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","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1038/s41467-021-23506-0","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000659145000011"]},"publication_identifier":{"eissn":["2041-1723"]},"month":"05","volume":12,"date_updated":"2023-08-08T13:53:53Z","date_created":"2021-05-28T14:25:50Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"first_name":"Nadia","last_name":"Nikulin","full_name":"Nikulin, Nadia"},{"full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R.","last_name":"Feathers"},{"first_name":"Marco","last_name":"Klanschnig","full_name":"Klanschnig, Marco"},{"first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas"},{"full_name":"Johnson, Marc C.","first_name":"Marc C.","last_name":"Johnson"},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."}],"publisher":"Nature Research","department":[{"_id":"FlSc"}],"publication_status":"published","year":"2021","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).","file_date_updated":"2021-06-09T15:21:14Z","article_number":"3226","date_published":"2021-05-28T00:00:00Z","article_type":"original","citation":{"chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","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).","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"28","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","file":[{"date_created":"2021-06-09T15:21:14Z","date_updated":"2021-06-09T15:21:14Z","checksum":"53ccc53d09a9111143839dbe7784e663","success":1,"relation":"main_file","file_id":"9538","file_size":6166295,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_NatureCommunications_Obr.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 12","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9431","issue":"1","abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"type":"journal_article"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","date_published":"2021-07-25T00:00:00Z","article_type":"original","citation":{"chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371.","short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371"},"publication":"Journal of Fluid Mechanics","abstract":[{"text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2021_JournalFluidMechanics_Marensi.pdf","access_level":"open_access","file_size":4087358,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"9766","date_created":"2021-08-03T09:53:28Z","date_updated":"2021-08-03T09:53:28Z","checksum":"867ad077e45c181c2c5ec1311ba27c41","success":1}],"oa_version":"Published Version","intvolume":" 919","title":"Suppression of turbulence and travelling waves in a vertical heated pipe","status":"public","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9467","publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1017/jfm.2021.371","isi":1,"quality_controlled":"1","external_id":{"arxiv":["2008.13486"],"isi":["000653785000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-08-03T09:53:28Z","article_number":"A17","volume":919,"date_updated":"2023-08-08T13:58:41Z","date_created":"2021-06-06T22:01:30Z","author":[{"full_name":"Marensi, Elena","first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"full_name":"He, Shuisheng","last_name":"He","first_name":"Shuisheng"},{"full_name":"Willis, Ashley P.","first_name":"Ashley P.","last_name":"Willis"}],"publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","year":"2021"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9470","intvolume":" 30","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","ddc":["570"],"status":"public","file":[{"date_created":"2021-06-11T15:34:53Z","date_updated":"2021-06-11T15:34:53Z","checksum":"e6f4731365bde2614b333040a08265d8","success":1,"relation":"main_file","file_id":"9545","file_size":1031978,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_MolecularEcology_Berdan.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"citation":{"mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936"},"publication":"Molecular Ecology","page":"2710-2723","date_published":"2021-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2021","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Berdan, Emma L.","first_name":"Emma L.","last_name":"Berdan"},{"full_name":"Blanckaert, Alexandre","first_name":"Alexandre","last_name":"Blanckaert"},{"full_name":"Slotte, Tanja","last_name":"Slotte","first_name":"Tanja"},{"last_name":"Suh","first_name":"Alexander","full_name":"Suh, Alexander"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"full_name":"Fragata, Inês","first_name":"Inês","last_name":"Fragata"}],"volume":30,"date_created":"2021-06-06T22:01:31Z","date_updated":"2023-08-08T13:59:18Z","ec_funded":1,"file_date_updated":"2021-06-11T15:34:53Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000652056400001"]},"project":[{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1111/mec.15936","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"month":"06"},{"publication_identifier":{"issn":["08954801"]},"month":"05","doi":"10.1137/20M1313234","language":[{"iso":"eng"}],"external_id":{"isi":["000674142200022"],"arxiv":["2001.06053"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.06053"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","ec_funded":1,"author":[{"full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","first_name":"Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Richter, R. Bruce","last_name":"Richter","first_name":"R. Bruce"},{"last_name":"Sunohara","first_name":"Matthew","full_name":"Sunohara, Matthew"}],"volume":35,"date_updated":"2023-08-08T13:58:12Z","date_created":"2021-06-06T22:01:30Z","year":"2021","department":[{"_id":"UlWa"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2021-05-20T00:00:00Z","citation":{"chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234.","short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234.","apa":"Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234","ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234"},"publication":"SIAM Journal on Discrete Mathematics","page":"1050-1076","article_type":"original","issue":"2","abstract":[{"lang":"eng","text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n"}],"type":"journal_article","oa_version":"Preprint","_id":"9468","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 35","status":"public","title":"Extending drawings of complete graphs into arrangements of pseudocircles"},{"date_created":"2021-06-06T22:01:28Z","date_updated":"2023-08-08T13:56:27Z","volume":281,"author":[{"full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Elsevier","acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","year":"2021","ec_funded":1,"article_number":"109096","language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2021.109096","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"main_file_link":[{"url":"https://arxiv.org/abs/2009.00992","open_access":"1"}],"month":"09","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"oa_version":"Preprint","title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","status":"public","intvolume":" 281","_id":"9462","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"}],"issue":"6","type":"journal_article","date_published":"2021-09-15T00:00:00Z","article_type":"original","publication":"Journal of Functional Analysis","citation":{"ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096."},"day":"15","article_processing_charge":"No","scopus_import":"1"}]