[{"abstract":[{"text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.","lang":"eng"}],"publication":"Frontiers in Cell and Developmental Biology","title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","department":[{"_id":"CaHe"}],"publisher":"Frontiers Media","date_created":"2021-05-09T22:01:37Z","oa_version":"Published Version","acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","status":"public","oa":1,"external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"article_type":"original","citation":{"mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9, 649433, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>.","ieee":"M. Bolger-Munro <i>et al.</i>, “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9. Frontiers Media, 2021."},"publication_identifier":{"eissn":["2296-634X"]},"volume":9,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"9379","has_accepted_license":"1","year":"2021","author":[{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","orcid":"0000-0002-8176-4824","first_name":"Madison"},{"first_name":"Kate","last_name":"Choi","full_name":"Choi, Kate"},{"first_name":"Faith","last_name":"Cheung","full_name":"Cheung, Faith"},{"first_name":"Yi Tian","last_name":"Liu","full_name":"Liu, Yi Tian"},{"last_name":"Dang-Lawson","first_name":"May","full_name":"Dang-Lawson, May"},{"full_name":"Deretic, Nikola","first_name":"Nikola","last_name":"Deretic"},{"last_name":"Keane","first_name":"Connor","full_name":"Keane, Connor"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"date_published":"2021-04-13T00:00:00Z","article_processing_charge":"No","date_updated":"2023-10-18T08:19:49Z","doi":"10.3389/fcell.2021.649433","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-05-11T15:09:23Z","article_number":"649433","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"ddc":["570"],"day":"13","month":"04","isi":1,"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"         9","file":[{"access_level":"open_access","creator":"kschuh","relation":"main_file","success":1,"date_created":"2021-05-11T15:09:23Z","content_type":"application/pdf","file_id":"9386","date_updated":"2021-05-11T15:09:23Z","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","checksum":"8c8a03575d2f7583f88dc3b658b0976b","file_size":4076024}],"publication_status":"published"},{"abstract":[{"text":"Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.","lang":"eng"}],"department":[{"_id":"FyKo"}],"title":"High rates of genome rearrangements and pathogenicity of Shigella spp","publication":"Frontiers in Microbiology","publisher":"Frontiers","oa_version":"Published Version","date_created":"2021-05-09T22:01:38Z","ec_funded":1,"status":"public","acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","oa":1,"article_type":"original","external_id":{"isi":["000643713300001"]},"citation":{"apa":"Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>","ieee":"Z. Seferbekova <i>et al.</i>, “High rates of genome rearrangements and pathogenicity of Shigella spp,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.","chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmicb.2021.628622\">https://doi.org/10.3389/fmicb.2021.628622</a>.","ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622.","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers in Microbiology</i>, vol. 12, 628622, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>.","ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fmicb.2021.628622\">10.3389/fmicb.2021.628622</a>"},"publication_identifier":{"eissn":["1664-302X"]},"volume":12,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9380","year":"2021","has_accepted_license":"1","author":[{"first_name":"Zaira","last_name":"Seferbekova","full_name":"Seferbekova, Zaira"},{"first_name":"Alexey","last_name":"Zabelkin","full_name":"Zabelkin, Alexey"},{"last_name":"Yakovleva","first_name":"Yulia","full_name":"Yakovleva, Yulia"},{"full_name":"Afasizhev, Robert","last_name":"Afasizhev","first_name":"Robert"},{"full_name":"Dranenko, Natalia O.","last_name":"Dranenko","first_name":"Natalia O."},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga"}],"date_published":"2021-04-12T00:00:00Z","doi":"10.3389/fmicb.2021.628622","date_updated":"2023-08-08T13:30:39Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-05-11T13:05:52Z","article_number":"628622","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"12","ddc":["570"],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"language":[{"iso":"eng"}],"isi":1,"month":"04","intvolume":"        12","publication_status":"published","file":[{"creator":"kschuh","access_level":"open_access","relation":"main_file","date_created":"2021-05-11T13:05:52Z","success":1,"content_type":"application/pdf","date_updated":"2021-05-11T13:05:52Z","file_id":"9384","checksum":"2f856543add59273a482a7f326fc0400","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","file_size":14362316}]},{"intvolume":"        17","publication_status":"published","file":[{"content_type":"application/pdf","date_created":"2021-05-11T13:50:06Z","success":1,"relation":"main_file","access_level":"open_access","creator":"kschuh","file_size":1323820,"checksum":"a94ebe0c4116f5047eaa6029e54d2dac","file_name":"2021_pcbi_Kleshnina.pdf","date_updated":"2021-05-11T13:50:06Z","file_id":"9385"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"language":[{"iso":"eng"}],"isi":1,"month":"04","day":"01","ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-05-11T13:50:06Z","article_number":"e1008523","scopus_import":"1","quality_controlled":"1","date_published":"2021-04-01T00:00:00Z","author":[{"last_name":"Kleshnina","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"full_name":"Streipert, Sabrina S.","last_name":"Streipert","first_name":"Sabrina S."},{"last_name":"Filar","first_name":"Jerzy A.","full_name":"Filar, Jerzy A."},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"}],"doi":"10.1371/journal.pcbi.1008523","date_updated":"2025-07-14T09:10:04Z","article_processing_charge":"No","_id":"9381","year":"2021","has_accepted_license":"1","volume":17,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., &#38; Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>","chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">https://doi.org/10.1371/journal.pcbi.1008523</a>.","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” <i>PLoS Computational Biology</i>, vol. 17, no. 4. Public Library of Science, 2021.","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” <i>PLoS Computational Biology</i>, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>.","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (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.","ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. <i>PLoS Computational Biology</i>. 2021;17(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008523\">10.1371/journal.pcbi.1008523</a>"},"publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"status":"public","acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","oa":1,"external_id":{"isi":["000639711200001"]},"article_type":"original","issue":"4","oa_version":"Published Version","date_created":"2021-05-09T22:01:38Z","ec_funded":1,"title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","department":[{"_id":"KrCh"}],"publication":"PLoS Computational Biology","publisher":"Public Library of Science","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."}]},{"day":"22","ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"month":"03","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","file":[{"creator":"kschuh","access_level":"open_access","relation":"main_file","success":1,"date_created":"2022-03-25T12:02:04Z","content_type":"application/pdf","file_id":"10921","date_updated":"2022-03-25T12:02:04Z","file_name":"2021_Evolution_Stankowski.pdf","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_size":719991}],"intvolume":"        75","doi":"10.1111/evo.14215","date_updated":"2023-10-18T08:16:01Z","article_processing_charge":"No","date_published":"2021-03-22T00:00:00Z","author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"}],"quality_controlled":"1","scopus_import":"1","file_date_updated":"2022-03-25T12:02:04Z","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"external_id":{"isi":["000647226400001"]},"article_type":"original","issue":"6","oa":1,"status":"public","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"citation":{"apa":"Stankowski, S., &#38; Ravinet, M. (2021). Defining the speciation continuum. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. <i>Evolution</i>. 2021;75(6):1256-1273. doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1256-1273","volume":75,"year":"2021","has_accepted_license":"1","_id":"9383","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"publisher":"Oxford University Press","title":"Defining the speciation continuum","department":[{"_id":"NiBa"}],"publication":"Evolution","oa_version":"Published Version","date_created":"2021-05-09T22:01:39Z"},{"abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"oa_version":"Preprint","date_created":"2021-05-12T05:58:42Z","publisher":"Elsevier ","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","department":[{"_id":"GradSch"}],"publication":"Journal of Theoretical Biology","publication_identifier":{"issn":["0022-5193"]},"citation":{"ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","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.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>.","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.","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier , 2021.","chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>"},"external_id":{"isi":["000659161500002"]},"article_type":"original","status":"public","oa":1,"acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","year":"2021","_id":"9387","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":524,"quality_controlled":"1","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"],"doi":"10.1016/j.jtbi.2021.110729","date_updated":"2023-08-08T13:32:40Z","article_processing_charge":"No","author":[{"last_name":"Khudiakova","orcid":"0000-0002-6246-1465","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia"},{"full_name":"Neretina, Tatiana Yu.","last_name":"Neretina","first_name":"Tatiana Yu."},{"full_name":"Kondrashov, Alexey S.","first_name":"Alexey S.","last_name":"Kondrashov"}],"date_published":"2021-04-24T00:00:00Z","article_number":"110729","language":[{"iso":"eng"}],"month":"04","isi":1,"day":"24","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"intvolume":"       524"},{"related_material":{"record":[{"id":"8910","status":"public","relation":"used_in_publication"}]},"date_updated":"2024-02-21T12:40:09Z","doi":"10.15479/AT:ISTA:9389","article_processing_charge":"No","date_published":"2021-01-01T00:00:00Z","author":[{"full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini"}],"abstract":[{"text":"This .zip File contains the transport data for  \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al.  \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\".","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","file_date_updated":"2021-05-14T11:56:48Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","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)"},"date_created":"2021-05-14T12:07:53Z","ddc":["530"],"status":"public","oa":1,"citation":{"apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>","chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>.","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","short":"M. Valentini, (2021).","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","mla":"Valentini, Marco. <i>Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>"},"contributor":[{"first_name":"Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person"}],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","year":"2021","file":[{"file_name":"Notebook_Valentini.pdf","checksum":"80a905c4eef24dab6fb247e81a3d67f5","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","file_id":"9390","date_created":"2021-05-14T11:42:23Z","content_type":"application/pdf","access_level":"open_access","creator":"mvalenti","relation":"main_file"},{"content_type":"application/x-zip-compressed","date_created":"2021-05-14T11:56:48Z","relation":"main_file","access_level":"open_access","creator":"mvalenti","file_size":99076111,"file_name":"Experimental_data.zip","checksum":"1e61a7e63949448a8db0091cdac23570","file_id":"9391","date_updated":"2021-05-14T11:56:48Z"}],"_id":"9389"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":31,"page":"R428-R429","year":"2021","_id":"9392","issue":"9","external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"article_type":"original","oa":1,"status":"public","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.","publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"citation":{"apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>"},"publisher":"Cell Press","publication":"Current Biology","title":"Quantifying the use of species concepts","department":[{"_id":"NiBa"}],"date_created":"2021-05-16T22:01:46Z","oa_version":"Published Version","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"}],"publication_status":"published","intvolume":"        31","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"day":"10","pmid":1,"isi":1,"month":"05","language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2023-08-08T13:34:38Z","doi":"10.1016/j.cub.2021.03.060","author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"date_published":"2021-05-10T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"article_type":"original","external_id":{"arxiv":["1504.07384"],"isi":["000645490300001"]},"status":"public","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","oa":1,"publication_identifier":{"eissn":["1572-8102"],"issn":["0925-9856"]},"citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>, vol. 57, Springer, 2021, pp. 401–28, doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. 2021;57:401-428. doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” <i>Formal Methods in System Design</i>, vol. 57. Springer, pp. 401–428, 2021.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"401-428","volume":57,"year":"2021","_id":"9393","arxiv":1,"abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"title":"Faster algorithms for quantitative verification in bounded treewidth graphs","publication":"Formal Methods in System Design","oa_version":"Preprint","date_created":"2021-05-16T22:01:47Z","ec_funded":1,"day":"01","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"09","isi":1,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1504.07384","open_access":"1"}],"intvolume":"        57","date_updated":"2023-10-10T11:13:20Z","doi":"10.1007/s10703-021-00373-5","article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"}],"date_published":"2021-09-01T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"date_updated":"2023-08-08T13:34:08Z","related_material":{"record":[{"id":"12987","status":"public","relation":"research_data"}]},"doi":"10.1002/evl3.227","article_processing_charge":"No","date_published":"2021-05-07T00:00:00Z","author":[{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"quality_controlled":"1","scopus_import":"1","file_date_updated":"2021-10-15T08:26:02Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"07","ddc":["570"],"project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"05","isi":1,"publication_status":"published","file":[{"success":1,"date_created":"2021-10-15T08:26:02Z","content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","relation":"main_file","file_name":"2021_EvolutionLetters_Koch.pdf","checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_size":3021108,"file_id":"10142","date_updated":"2021-10-15T08:26:02Z"}],"intvolume":"         5","abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"publisher":"Wiley","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"publication":"Evolution Letters","oa_version":"Published Version","date_created":"2021-05-16T22:01:47Z","ec_funded":1,"external_id":{"isi":["000647846200001"]},"article_type":"original","issue":"3","oa":1,"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. ","status":"public","publication_identifier":{"eissn":["2056-3744"]},"citation":{"ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. 2021;5(3):196-213. doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>.","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.","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.","ieee":"E. L. Koch <i>et al.</i>, “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” <i>Evolution Letters</i>, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>"},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"196-213","volume":5,"has_accepted_license":"1","year":"2021","_id":"9394"},{"file":[{"file_size":47799741,"file_name":"KHuljev_Thesis_corrections.docx","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398","date_updated":"2022-05-21T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2021-05-17T12:29:12Z","relation":"source_file","creator":"khuljev","access_level":"closed"},{"date_updated":"2022-05-21T22:30:04Z","file_id":"9401","embargo":"2022-05-20","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_name":"new_KHuljev_Thesis_corrections.pdf","file_size":16542131,"creator":"khuljev","access_level":"open_access","relation":"main_file","date_created":"2021-05-18T14:50:28Z","content_type":"application/pdf"}],"publication_status":"published","month":"05","language":[{"iso":"eng"}],"ddc":["571"],"day":"18","file_date_updated":"2022-05-21T22:30:04Z","degree_awarded":"PhD","article_processing_charge":"No","doi":"10.15479/at:ista:9397","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T13:32:32Z","date_published":"2021-05-18T00:00:00Z","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla"}],"has_accepted_license":"1","year":"2021","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"_id":"9397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","page":"101","publication_identifier":{"issn":["2663-337X"]},"citation":{"ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria."},"oa":1,"status":"public","date_created":"2021-05-17T12:31:30Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}]},{"file_date_updated":"2023-11-07T08:27:23Z","article_processing_charge":"No","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/"}],"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}]},"doi":"10.1038/s41562-021-01114-8","date_updated":"2025-07-14T09:10:09Z","date_published":"2021-05-13T00:00:00Z","author":[{"first_name":"Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"quality_controlled":"1","scopus_import":"1","file":[{"file_size":5232761,"file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","checksum":"34f55e173f90dc1dab731063458ac780","file_id":"14496","date_updated":"2023-11-07T08:27:23Z","content_type":"application/pdf","success":1,"date_created":"2023-11-07T08:27:23Z","relation":"main_file","creator":"dernst","access_level":"open_access"}],"publication_status":"published","intvolume":"         5","ddc":["000"],"day":"13","pmid":1,"month":"05","isi":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","publication":"Nature Human Behaviour","title":"A unified framework of direct and indirect reciprocity","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_created":"2021-05-18T16:56:57Z","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":5,"page":"1292–1302","has_accepted_license":"1","year":"2021","_id":"9402","issue":"10","article_type":"original","external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"status":"public","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","oa":1,"publication_identifier":{"eissn":["2397-3374"]},"citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <i>Nature Human Behaviour</i>, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302."}},{"day":"01","oa":1,"status":"public","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-0-262-04559-9"]},"month":"03","citation":{"apa":"Schmid, L., &#38; Hilbe, C. (2021). The evolution of strategic ignorance in strategic interaction. In R. Hertwig &#38; C. Engel (Eds.), <i>Deliberate Ignorance: Choosing Not To Know</i> (Vol. 29, pp. 139–152). MIT Press.","chicago":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” In <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, 29:139–52. Strüngmann Forum Reports. MIT Press, 2021.","ieee":"L. Schmid and C. Hilbe, “The evolution of strategic ignorance in strategic interaction,” in <i>Deliberate Ignorance: Choosing Not To Know</i>, vol. 29, R. Hertwig and C. Engel, Eds. MIT Press, 2021, pp. 139–152.","ista":"Schmid L, Hilbe C. 2021.The evolution of strategic ignorance in strategic interaction. In: Deliberate Ignorance: Choosing Not To Know. vol. 29, 139–152.","mla":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, vol. 29, MIT Press, 2021, pp. 139–52.","short":"L. Schmid, C. Hilbe, in:, R. Hertwig, C. Engel (Eds.), Deliberate Ignorance: Choosing Not To Know, MIT Press, 2021, pp. 139–152.","ama":"Schmid L, Hilbe C. The evolution of strategic ignorance in strategic interaction. In: Hertwig R, Engel C, eds. <i>Deliberate Ignorance: Choosing Not To Know</i>. Vol 29. Strüngmann Forum Reports. MIT Press; 2021:139-152."},"type":"book_chapter","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"139-152","volume":29,"year":"2021","intvolume":"        29","_id":"9403","main_file_link":[{"url":"https://esforum.de/publications/PDFs/sfr29/SFR29_09_Hilbe%20and%20Schmid.pdf","open_access":"1"}],"date_updated":"2023-02-23T13:57:04Z","article_processing_charge":"No","editor":[{"full_name":"Hertwig, Ralph","first_name":"Ralph","last_name":"Hertwig"},{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"}],"date_published":"2021-03-01T00:00:00Z","author":[{"orcid":"0000-0002-6978-7329","last_name":"Schmid","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"}],"quality_controlled":"1","series_title":"Strüngmann Forum Reports","abstract":[{"lang":"eng","text":"Optimal decision making requires individuals to know their available options and to anticipate correctly what consequences these options have. In many social interactions, however, we refrain from gathering all relevant information, even if this information would help us make better decisions and is costless to obtain. This chapter examines several examples of “deliberate ignorance.” Two simple models are proposed to illustrate how ignorance can evolve among self-interested and payoff - maximizing individuals, and open problems are highlighted that lie ahead for future research to explore."}],"publisher":"MIT Press","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"title":"The evolution of strategic ignorance in strategic interaction","publication":"Deliberate Ignorance: Choosing Not To Know","oa_version":"Published Version","date_created":"2021-05-19T12:25:42Z"},{"publication_status":"published","file":[{"relation":"main_file","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","date_created":"2021-05-25T14:18:40Z","success":1,"file_id":"9426","date_updated":"2021-05-25T14:18:40Z","file_size":1176573,"checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","file_name":"2021_NatureCommunications_Scarselli.pdf"}],"intvolume":"        12","language":[{"iso":"eng"}],"isi":1,"month":"05","day":"10","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"2586","file_date_updated":"2021-05-25T14:18:40Z","quality_controlled":"1","scopus_import":"1","doi":"10.1038/s41467-021-22725-9","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/smashing-the-covid-curve/"}]},"date_updated":"2023-08-08T13:45:13Z","article_processing_charge":"No","date_published":"2021-05-10T00:00:00Z","author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide"},{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Timme, Marc","first_name":"Marc","last_name":"Timme"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"has_accepted_license":"1","year":"2021","_id":"9407","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":12,"publication_identifier":{"eissn":["20411723"]},"citation":{"apa":"Scarselli, D., Budanur, N. B., Timme, M., &#38; Hof, B. (2021). Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>.","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586.","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>.","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>"},"article_type":"original","external_id":{"isi":["000687305500044"]},"issue":"1","status":"public","oa":1,"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.","oa_version":"Published Version","date_created":"2021-05-23T22:01:42Z","publisher":"Springer Nature","title":"Discontinuous epidemic transition due to limited testing","department":[{"_id":"BjHo"}],"publication":"Nature Communications","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"}]},{"intvolume":"        27","file":[{"success":1,"date_created":"2021-05-25T15:08:49Z","content_type":"application/pdf","creator":"kschuh","access_level":"open_access","relation":"main_file","file_name":"2021_TVCG_Feng.pdf","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","file_size":6183002,"file_id":"9427","date_updated":"2021-05-25T15:08:49Z"}],"publication_status":"published","pmid":1,"ddc":["000"],"day":"01","month":"06","isi":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2021-05-25T15:08:49Z","article_number":"2881-2895","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-06-01T00:00:00Z","author":[{"last_name":"Feng","first_name":"Xudong","full_name":"Feng, Xudong"},{"full_name":"Liu, Jiafeng","last_name":"Liu","first_name":"Jiafeng"},{"full_name":"Wang, Huamin","first_name":"Huamin","last_name":"Wang"},{"full_name":"Yang, Yin","last_name":"Yang","first_name":"Yin"},{"first_name":"Hujun","last_name":"Bao","full_name":"Bao, Hujun"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"article_processing_charge":"No","date_updated":"2023-08-08T13:45:46Z","doi":"10.1109/TVCG.2019.2957218","scopus_import":"1","quality_controlled":"1","volume":27,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9408","has_accepted_license":"1","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).","status":"public","oa":1,"issue":"6","external_id":{"pmid":["31804937"],"isi":["000649620700009"]},"citation":{"ieee":"X. Feng <i>et al.</i>, “Computational design of skinned Quad-Robots,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 27, no. 6. IEEE, 2021.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">https://doi.org/10.1109/TVCG.2019.2957218</a>.","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., &#38; Xu, W. (2021). Computational design of skinned Quad-Robots. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">https://doi.org/10.1109/TVCG.2019.2957218</a>","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2021;27(6). doi:<a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">10.1109/TVCG.2019.2957218</a>","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:<a href=\"https://doi.org/10.1109/TVCG.2019.2957218\">10.1109/TVCG.2019.2957218</a>.","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."},"publication_identifier":{"issn":["19410506"],"eissn":["10772626"]},"publication":"IEEE Transactions on Visualization and Computer Graphics","title":"Computational design of skinned Quad-Robots","department":[{"_id":"BeBi"}],"publisher":"IEEE","date_created":"2021-05-23T22:01:42Z","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype.","lang":"eng"}]},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"date_created":"2021-05-23T22:01:43Z","title":"Adaptation at different points along antibiotic concentration gradients","department":[{"_id":"NiBa"}],"publication":"Biology letters","publisher":"Royal Society of London","citation":{"ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” <i>Biology letters</i>, vol. 17, no. 5. Royal Society of London, 2021.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>. Royal Society of London, 2021. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>.","apa":"Lagator, M., Uecker, H., &#38; Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. <i>Biology letters</i>. 2021;17(5). doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021)."},"publication_identifier":{"eissn":["1744957X"]},"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.","status":"public","oa":1,"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"issue":"5","_id":"9410","year":"2021","has_accepted_license":"1","volume":17,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","quality_controlled":"1","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato"},{"last_name":"Uecker","orcid":"0000-0001-9435-2813","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"date_published":"2021-05-12T00:00:00Z","date_updated":"2025-05-28T11:42:50Z","doi":"10.1098/rsbl.2020.0913","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-05-25T14:09:03Z","article_number":"20200913","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"isi":1,"month":"05","pmid":1,"day":"12","ddc":["570"],"intvolume":"        17","publication_status":"published","file":[{"relation":"main_file","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2021-05-25T14:09:03Z","date_updated":"2021-05-25T14:09:03Z","file_id":"9425","file_size":726759,"file_name":"2021_BiologyLetters_Lagator.pdf","checksum":"9c13c1f5af7609c97c741f11d293188a"}]},{"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"}],"publication":"European Physical Journal E","title":"Regimes of motion of magnetocapillary swimmers","department":[{"_id":"ScWa"}],"publisher":"Springer","date_created":"2021-05-23T22:01:44Z","oa_version":"Published Version","status":"public","oa":1,"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.","issue":"4","external_id":{"isi":["000643251300001"]},"citation":{"ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. <i>European Physical Journal E</i>. 2021;44(4). doi:<a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">10.1140/epje/s10189-021-00065-2</a>","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.","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” <i>European Physical Journal E</i>, vol. 44, no. 4, 59, Springer, 2021, doi:<a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">10.1140/epje/s10189-021-00065-2</a>.","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” <i>European Physical Journal E</i>. Springer, 2021. <a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">https://doi.org/10.1140/epje/s10189-021-00065-2</a>.","ieee":"A. Sukhov <i>et al.</i>, “Regimes of motion of magnetocapillary swimmers,” <i>European Physical Journal E</i>, vol. 44, no. 4. Springer, 2021.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. <i>European Physical Journal E</i>. Springer. <a href=\"https://doi.org/10.1140/epje/s10189-021-00065-2\">https://doi.org/10.1140/epje/s10189-021-00065-2</a>"},"publication_identifier":{"issn":["12928941"],"eissn":["1292895X"]},"volume":44,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9411","has_accepted_license":"1","year":"2021","date_published":"2021-04-24T00:00:00Z","author":[{"last_name":"Sukhov","first_name":"Alexander","full_name":"Sukhov, Alexander"},{"first_name":"Maxime","last_name":"Hubert","full_name":"Hubert, Maxime"},{"full_name":"Grosjean, Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean"},{"first_name":"Oleg","last_name":"Trosman","full_name":"Trosman, Oleg"},{"full_name":"Ziegler, Sebastian","last_name":"Ziegler","first_name":"Sebastian"},{"first_name":"Ylona","last_name":"Collard","full_name":"Collard, Ylona"},{"last_name":"Vandewalle","first_name":"Nicolas","full_name":"Vandewalle, Nicolas"},{"first_name":"Ana Sunčana","last_name":"Smith","full_name":"Smith, Ana Sunčana"},{"first_name":"Jens","last_name":"Harting","full_name":"Harting, Jens"}],"article_processing_charge":"No","doi":"10.1140/epje/s10189-021-00065-2","date_updated":"2023-08-08T13:36:28Z","scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-05-25T11:32:14Z","article_number":"59","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"day":"24","isi":1,"month":"04","language":[{"iso":"eng"}],"intvolume":"        44","file":[{"file_id":"9422","date_updated":"2021-05-25T11:32:14Z","file_size":2507870,"checksum":"0ef342d011afbe3c5cb058fda9a3f395","file_name":"2021_EPJE_Sukhov.pdf","relation":"main_file","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","date_created":"2021-05-25T11:32:14Z","success":1}],"publication_status":"published"},{"oa_version":"Published Version","date_created":"2021-05-23T22:01:44Z","ec_funded":1,"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"title":"Fluctuation around the circular law for random matrices with real entries","publication":"Electronic Journal of Probability","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."}],"arxiv":1,"has_accepted_license":"1","year":"2021","_id":"9412","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":26,"publication_identifier":{"eissn":["10836489"]},"citation":{"apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>.","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.” <i>Electronic Journal of Probability</i>, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>.","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. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>"},"external_id":{"isi":["000641855600001"],"arxiv":["2002.02438"]},"oa":1,"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"24","file_date_updated":"2021-05-25T13:24:19Z","quality_controlled":"1","scopus_import":"1","doi":"10.1214/21-EJP591","date_updated":"2023-08-08T13:39:19Z","article_processing_charge":"No","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","first_name":"Giorgio"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-03-23T00:00:00Z","publication_status":"published","file":[{"file_id":"9423","date_updated":"2021-05-25T13:24:19Z","file_name":"2021_EJP_Cipolloni.pdf","checksum":"864ab003ad4cffea783f65aa8c2ba69f","file_size":865148,"access_level":"open_access","creator":"kschuh","relation":"main_file","success":1,"date_created":"2021-05-25T13:24:19Z","content_type":"application/pdf"}],"intvolume":"        26","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"language":[{"iso":"eng"}],"isi":1,"month":"03","day":"23","ddc":["510"]},{"tmp":{"short":"CC BY-NC-SA (3.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"},"article_processing_charge":"No","doi":"10.1091/MBC.E20-11-0723","date_updated":"2023-08-08T13:36:02Z","author":[{"last_name":"Ishihara","first_name":"Keisuke","full_name":"Ishihara, Keisuke"},{"full_name":"Decker, Franziska","last_name":"Decker","first_name":"Franziska"},{"full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461"},{"last_name":"Pelletier","first_name":"James F.","full_name":"Pelletier, James F."},{"last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"full_name":"Mitchison, Timothy J.","first_name":"Timothy J.","last_name":"Mitchison"}],"date_published":"2021-04-19T00:00:00Z","quality_controlled":"1","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"intvolume":"        32","day":"19","isi":1,"month":"04","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publisher":"American Society for Cell Biology","publication":"Molecular Biology of the Cell","department":[{"_id":"MaLo"}],"title":"Spatial variation of microtubule depolymerization in large asters","date_created":"2021-05-23T22:01:45Z","ec_funded":1,"oa_version":"Published Version","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":32,"page":"869-879","year":"2021","_id":"9414","issue":"9","article_type":"original","external_id":{"isi":["000641574700005"]},"status":"public","oa":1,"acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"citation":{"ieee":"K. Ishihara <i>et al.</i>, “Spatial variation of microtubule depolymerization in large asters,” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2021. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., &#38; Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. 2021;32(9):869-879. doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>","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.","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.","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>."}},{"citation":{"ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: <i>9th International Conference on Learning Representations</i>. ; 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations.  ICLR: International Conference on Learning Representations.","short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” <i>9th International Conference on Learning Representations</i>, 2021.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In <i>9th International Conference on Learning Representations</i>, 2021.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in <i>9th International Conference on Learning Representations</i>, Virtual, 2021.","apa":"Phuong, M., &#38; Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In <i>9th International Conference on Learning Representations</i>. Virtual."},"month":"05","language":[{"iso":"eng"}],"oa":1,"status":"public","ddc":["000"],"day":"01","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"_id":"9416","has_accepted_license":"1","file":[{"relation":"main_file","creator":"bphuong","access_level":"open_access","content_type":"application/pdf","date_created":"2021-05-24T11:15:57Z","date_updated":"2021-05-24T11:15:57Z","file_id":"9417","file_size":502356,"checksum":"f34ff17017527db5ba6927f817bdd125","file_name":"iclr2021_conference.pdf"}],"year":"2021","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","abstract":[{"lang":"eng","text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time  onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks."}],"scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"date_published":"2021-05-01T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9418"}]},"date_updated":"2023-09-07T13:29:50Z","date_created":"2021-05-24T11:16:46Z","conference":{"start_date":"2021-05-03","location":"Virtual","end_date":"2021-05-07","name":" ICLR: International Conference on Learning Representations"},"oa_version":"Published Version","publication":"9th International Conference on Learning Representations","title":"The inductive bias of ReLU networks on orthogonally separable data","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file_date_updated":"2021-05-24T11:15:57Z"},{"citation":{"ama":"Phuong M. Underspecification in deep learning. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>","mla":"Phuong, Mary. <i>Underspecification in Deep Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","apa":"Phuong, M. (2021). <i>Underspecification in deep learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>"},"publication_identifier":{"issn":["2663-337X"]},"oa":1,"status":"public","supervisor":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"_id":"9418","has_accepted_license":"1","year":"2021","page":"125","type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models.","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-05-24T13:06:23Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"title":"Underspecification in deep learning","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"month":"05","day":"30","ddc":["000"],"publication_status":"published","file":[{"date_updated":"2021-05-24T11:22:29Z","file_id":"9419","file_size":2673905,"checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_name":"mph-thesis-v519-pdfimages.pdf","relation":"main_file","creator":"bphuong","access_level":"open_access","content_type":"application/pdf","date_created":"2021-05-24T11:22:29Z","success":1},{"file_id":"9420","date_updated":"2021-05-24T11:56:02Z","checksum":"f5699e876bc770a9b0df8345a77720a2","file_name":"thesis.zip","file_size":92995100,"access_level":"closed","creator":"bphuong","relation":"source_file","date_created":"2021-05-24T11:56:02Z","content_type":"application/zip"}],"degree_awarded":"PhD","date_published":"2021-05-30T00:00:00Z","author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai"}],"date_updated":"2023-09-08T11:11:12Z","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:9418","related_material":{"record":[{"status":"deleted","relation":"part_of_dissertation","id":"7435"},{"id":"7481","status":"public","relation":"part_of_dissertation"},{"id":"9416","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7479"}]},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"file_date_updated":"2021-05-24T11:56:02Z"}]