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As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n"}],"issue":"11","publication":"Ecography","citation":{"mla":"Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444","ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. 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L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151."},"publication":"BioEssays","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"6939","checksum":"8cc7551bff70b2658f8d5630f228ee12","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","access_level":"open_access","file_name":"2019_BioEssays_Giese.pdf","content_type":"application/pdf","file_size":193248,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 41","ddc":["570"],"title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","status":"public","_id":"6857","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"type":"journal_article"},{"volume":105,"date_created":"2019-09-18T08:15:37Z","date_updated":"2023-08-30T06:56:00Z","author":[{"full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"department":[{"_id":"FlSc"}],"editor":[{"full_name":"Rey, Félix A.","last_name":"Rey","first_name":"Félix A."}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1016/bs.aivir.2019.07.008","isi":1,"quality_controlled":"1","external_id":{"isi":["000501594500006"],"pmid":[" 31522703"]},"abstract":[{"text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.","lang":"eng"}],"type":"book_chapter","oa_version":"None","intvolume":" 105","status":"public","title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","_id":"6890","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"27","series_title":"Advances in Virus Research","scopus_import":"1","date_published":"2019-08-27T00:00:00Z","page":"117-159","citation":{"ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in Complementary Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159.","apa":"Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008","mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008."},"publication":"Complementary Strategies to Study Virus Structure and Function"},{"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.123.100601","project":[{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.06253"}],"external_id":{"isi":["000483587200004"],"arxiv":["1907.06253"]},"article_number":"100601","volume":123,"date_updated":"2023-08-30T06:57:53Z","date_created":"2019-10-14T06:31:13Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/","description":"News auf IST Website","relation":"press_release"}]},"author":[{"orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo"},{"last_name":"Defenu","first_name":"Nicolò","full_name":"Defenu, Nicolò"},{"full_name":"Nándori, István","last_name":"Nándori","first_name":"István"},{"first_name":"Luca","last_name":"Salasnich","full_name":"Salasnich, Luca"},{"full_name":"Trombettoni, Andrea","last_name":"Trombettoni","first_name":"Andrea"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2019","acknowledgement":"We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged.","article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2019-09-06T00:00:00Z","article_type":"original","citation":{"ama":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 2019;123(10). doi:10.1103/physrevlett.123.100601","apa":"Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601","ieee":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019.","ista":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.","short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019).","mla":"Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601.","chicago":"Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601."},"publication":"Physical Review Letters","issue":"10","abstract":[{"text":"We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 123","status":"public","title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","_id":"6940","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:44Z","article_number":"eaaw6490","volume":5,"date_created":"2019-09-29T22:00:45Z","date_updated":"2023-08-30T06:55:31Z","author":[{"first_name":"Chao","last_name":"Qi","full_name":"Qi, Chao"},{"full_name":"Minin, Giulio Di","last_name":"Minin","first_name":"Giulio Di"},{"last_name":"Vercellino","first_name":"Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene"},{"first_name":"Anton","last_name":"Wutz","full_name":"Wutz, Anton"},{"first_name":"Volodymyr M.","last_name":"Korkhov","full_name":"Korkhov, Volodymyr M."}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"publication_status":"published","year":"2019","publication_identifier":{"eissn":["23752548"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aaw6490","quality_controlled":"1","isi":1,"external_id":{"isi":["000491128800062"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"issue":"9","type":"journal_article","file":[{"file_name":"2019_AAAS_Qi.pdf","access_level":"open_access","file_size":1236101,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6928","date_created":"2019-10-02T11:13:54Z","date_updated":"2020-07-14T12:47:44Z","checksum":"b2256c9117655bc15f621ba0babf219f"}],"oa_version":"Published Version","intvolume":" 5","ddc":["570"],"status":"public","title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6919","article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","date_published":"2019-09-18T00:00:00Z","citation":{"short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019).","mla":"Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.","chicago":"Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw6490.","ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490","apa":"Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490","ieee":"C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","ista":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490."},"publication":"Science Advances"},{"abstract":[{"text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_FrontiersImmonology_Kelemen.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2083061,"file_id":"6984","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T15:54:00Z","checksum":"68d1708f7aa412544159b498ef17a6b9"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6983","intvolume":" 10","ddc":["570"],"title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"20","scopus_import":"1","date_published":"2019-09-20T00:00:00Z","citation":{"short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019.","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153."},"publication":"Frontiers in Immunology","article_type":"original","file_date_updated":"2020-07-14T12:47:46Z","article_number":"2153","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","first_name":"Réka K","last_name":"Kelemen","full_name":"Kelemen, Réka K"},{"first_name":"H","last_name":"Rajakaruna","full_name":"Rajakaruna, H"},{"full_name":"Cockburn, IA","first_name":"IA","last_name":"Cockburn"},{"full_name":"Ganusov, VV","first_name":"VV","last_name":"Ganusov"}],"volume":10,"date_updated":"2023-08-30T07:18:23Z","date_created":"2019-11-04T15:50:06Z","pmid":1,"year":"2019","department":[{"_id":"BeVi"}],"publisher":"Frontiers","publication_status":"published","publication_identifier":{"issn":["1664-3224"]},"month":"09","doi":"10.3389/fimmu.2019.02153","language":[{"iso":"eng"}],"external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1},{"file":[{"file_name":"2019_JACM_Lenzen.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2183085,"file_id":"6975","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-25T12:58:38Z","checksum":"7e5d95c478e0e393f4927fcf7e48194e"}],"oa_version":"Published Version","_id":"6972","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 66","status":"public","ddc":["000"],"title":"Self-stabilising Byzantine clock synchronisation is almost as easy as consensus","issue":"5","abstract":[{"text":"We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to fJournal of the ACM, vol. 66, no. 5, 32, ACM, 2019, doi:10.1145/3339471.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3339471.","ama":"Lenzen C, Rybicki J. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 2019;66(5). doi:10.1145/3339471","apa":"Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471","ieee":"C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM, 2019.","ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32."},"publication":"Journal of the ACM","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","author":[{"full_name":"Lenzen, Christoph","first_name":"Christoph","last_name":"Lenzen"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"}],"volume":66,"date_created":"2019-10-24T17:12:48Z","date_updated":"2023-08-30T07:07:23Z","year":"2019","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"32","doi":"10.1145/3339471","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1705.06173"],"isi":["000496514100001"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0004-5411"]},"month":"09"},{"publication_identifier":{"isbn":["9783030302801"],"issn":["0302-9743"],"eisbn":["9783030302818"]},"month":"09","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08178"}],"external_id":{"arxiv":["1906.08178"],"isi":["000679281300007"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-30281-8_7","conference":{"end_date":"2019-09-12","start_date":"2019-09-10","location":"Glasgow, United Kingdom","name":"QEST: Quantitative Evaluation of Systems"},"department":[{"_id":"KrCh"},{"_id":"ChLa"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","volume":11785,"date_created":"2019-10-14T06:57:49Z","date_updated":"2023-08-30T06:59:36Z","author":[{"full_name":"Ashok, Pranav","last_name":"Ashok","first_name":"Pranav"},{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Křetínský, Jan","last_name":"Křetínský","first_name":"Jan"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor"}],"scopus_import":"1","article_processing_charge":"No","day":"04","page":"109-128","citation":{"ama":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: 16th International Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature; 2019:109-128. doi:10.1007/978-3-030-30281-8_7","ista":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128.","apa":"Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., & Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In 16th International Conference on Quantitative Evaluation of Systems (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7","ieee":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in 16th International Conference on Quantitative Evaluation of Systems, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128.","mla":"Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” 16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.","short":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128.","chicago":"Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In 16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7."},"publication":"16th International Conference on Quantitative Evaluation of Systems","date_published":"2019-09-04T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees."}],"intvolume":" 11785","title":"Strategy representation by decision trees with linear classifiers","status":"public","_id":"6942","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1904.00913"],"isi":["000494939000086"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.physletb.2019.135016","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0370-2693"]},"month":"11","year":"2019","department":[{"_id":"MiLe"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Schmickler, C.H.","last_name":"Schmickler","first_name":"C.H."},{"full_name":"Hammer, H.-W.","first_name":"H.-W.","last_name":"Hammer"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"volume":798,"date_updated":"2023-08-30T07:06:42Z","date_created":"2019-10-18T18:33:32Z","article_number":"135016","file_date_updated":"2020-07-14T12:47:46Z","citation":{"ieee":"C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” Physics Letters B, vol. 798. Elsevier, 2019.","apa":"Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics of bound states of a few charged particles. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2019.135016","ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","ama":"Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016","chicago":"Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier, 2019. https://doi.org/10.1016/j.physletb.2019.135016.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","mla":"Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016."},"publication":"Physics Letters B","article_type":"original","date_published":"2019-11-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","_id":"6955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 798","title":"Universal physics of bound states of a few charged particles","ddc":["530"],"status":"public","file":[{"file_id":"6974","relation":"main_file","checksum":"d27f983b34ea7dafdf356afbf9472fbf","date_created":"2019-10-25T12:47:04Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_name":"2019_PhysicsLettersB_Schmickler.pdf","creator":"dernst","file_size":528362,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.","lang":"eng"}]},{"doi":"10.1111/jnc.14862","language":[{"iso":"eng"}],"external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0022-3042"],"eissn":["1471-4159"]},"month":"12","author":[{"full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"first_name":"Michael A.","last_name":"Cousin","full_name":"Cousin, Michael A."}],"volume":151,"date_created":"2019-11-12T14:37:08Z","date_updated":"2023-08-30T07:21:50Z","pmid":1,"year":"2019","publisher":"Wiley","department":[{"_id":"SiHi"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:47Z","date_published":"2019-12-01T00:00:00Z","citation":{"chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862.","apa":"Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862"},"publication":"Journal of Neurochemistry","page":"570-583","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"file_id":"7452","relation":"main_file","checksum":"ec1fb2aebb874009bc309adaada6e1d7","date_created":"2020-02-05T10:30:02Z","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","file_name":"2019_JournNeurochemistry_Cheung.pdf","creator":"dernst","file_size":4334962,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7005","intvolume":" 151","ddc":["570"],"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","status":"public","issue":"5","abstract":[{"lang":"eng","text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes."}],"type":"journal_article"},{"date_published":"2019-12-01T00:00:00Z","article_type":"original","citation":{"apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019.","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161.","ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9."},"publication":"Computational and Applied Mathematics","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","intvolume":" 38","title":"Convergence analysis of projection method for variational inequalities","ddc":["510","515","518"],"status":"public","_id":"7000","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","abstract":[{"lang":"eng","text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s40314-019-0955-9","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s40314-019-0955-9"}],"external_id":{"arxiv":["2101.09081"],"isi":["000488973100005"]},"publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"month":"12","volume":38,"date_updated":"2023-08-30T07:20:32Z","date_created":"2019-11-12T12:41:44Z","author":[{"first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini"},{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"full_name":"Li, Xiao-Huan","first_name":"Xiao-Huan","last_name":"Li"},{"first_name":"Qiao-Li","last_name":"Dong","full_name":"Dong, Qiao-Li"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","ec_funded":1,"article_number":"161"},{"type":"journal_article","abstract":[{"text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration.","lang":"eng"}],"issue":"12","_id":"7009","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Mechanisms of 3D cell migration","intvolume":" 20","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nature Reviews Molecular Cell Biology","citation":{"chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9.","short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","apa":"Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9"},"article_type":"review","page":"738–752","date_published":"2019-12-01T00:00:00Z","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","author":[{"full_name":"Yamada, KM","last_name":"Yamada","first_name":"KM"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"date_created":"2019-11-12T14:54:42Z","date_updated":"2023-08-30T07:22:20Z","volume":20,"month":"12","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41580-019-0172-9","language":[{"iso":"eng"}]},{"month":"10","publication_identifier":{"issn":["1471-4906"]},"quality_controlled":"1","isi":1,"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"external_id":{"pmid":["31601520"],"isi":["000493292100005"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.it.2019.08.004","ec_funded":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Cell Press","year":"2019","pmid":1,"date_updated":"2023-08-30T07:19:23Z","date_created":"2019-11-04T16:27:36Z","volume":40,"author":[{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"review","page":"922-938","publication":"Trends in Immunology","citation":{"chicago":"Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.","short":"L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.","mla":"Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004.","ieee":"L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.","apa":"Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004","ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","ama":"Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004"},"date_published":"2019-10-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth.","lang":"eng"}],"issue":"10","status":"public","title":"Platelets in host defense: Experimental and clinical insights","intvolume":" 40","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6988","oa_version":"None"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019)."},"article_type":"original","abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"None","_id":"7002","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Optimal multiple importance sampling","status":"public","intvolume":" 38","month":"07","publication_identifier":{"issn":["0730-0301"]},"doi":"10.1145/3306346.3323009","language":[{"iso":"eng"}],"external_id":{"isi":["000475740600011"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020"}],"ec_funded":1,"article_number":"37","author":[{"last_name":"Kondapaneni","first_name":"Ivo","full_name":"Kondapaneni, Ivo"},{"last_name":"Vevoda","first_name":"Petr","full_name":"Vevoda, Petr"},{"last_name":"Grittmann","first_name":"Pascal","full_name":"Grittmann, Pascal"},{"full_name":"Skrivan, Tomas","first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Slusallek, Philipp","last_name":"Slusallek","first_name":"Philipp"},{"full_name":"Křivánek, Jaroslav","last_name":"Křivánek","first_name":"Jaroslav"}],"date_created":"2019-11-12T13:05:40Z","date_updated":"2023-08-30T07:21:25Z","volume":38,"year":"2019","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM"},{"abstract":[{"text":"In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","status":"public","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","intvolume":" 4","_id":"6978","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"102401","publication":"Physical Review Fluids","citation":{"ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","apa":"Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids. American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401."},"date_updated":"2023-08-30T07:20:03Z","date_created":"2019-11-04T10:04:01Z","volume":4,"author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"last_name":"Dogra","first_name":"Akshunna","full_name":"Dogra, Akshunna"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"year":"2019","month":"10","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.4.102401","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]}}]