[{"author":[{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"first_name":"Adrien","last_name":"Hallou","full_name":"Hallou, Adrien"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"date_created":"2019-03-31T21:59:13Z","date_updated":"2023-08-25T08:57:30Z","volume":116,"year":"2019","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:47:23Z","doi":"10.1073/pnas.1813255116","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"month":"03","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"oa_version":"Published Version","file":[{"file_name":"2019_PNAS_Recho.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3456045,"creator":"dernst","relation":"main_file","file_id":"6193","date_created":"2019-04-03T14:10:30Z","date_updated":"2020-07-14T12:47:23Z","checksum":"8b67eee0ea8e5db61583e4d485215258"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6191","title":"Theory of mechanochemical patterning in biphasic biological tissues","status":"public","ddc":["570"],"intvolume":" 116","abstract":[{"text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.","lang":"eng"}],"issue":"12","type":"journal_article","date_published":"2019-03-19T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116","chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116."},"page":"5344-5349","day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1158/1541-7786.MCR-18-0530","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1158/1541-7786.MCR-18-0530","open_access":"1"}],"external_id":{"pmid":["30552233"],"isi":["000460099800012"]},"oa":1,"month":"03","publication_identifier":{"eissn":["15573125"],"issn":["15417786"]},"date_created":"2019-03-31T21:59:12Z","date_updated":"2023-08-25T08:57:01Z","volume":17,"author":[{"full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko","last_name":"Roblek"},{"full_name":"Protsyuk, Darya","last_name":"Protsyuk","first_name":"Darya"},{"full_name":"Becker, Paul F.","first_name":"Paul F.","last_name":"Becker"},{"full_name":"Stefanescu, Cristina","first_name":"Cristina","last_name":"Stefanescu"},{"full_name":"Gorzelanny, Christian","last_name":"Gorzelanny","first_name":"Christian"},{"full_name":"Glaus Garzon, Jesus F.","last_name":"Glaus Garzon","first_name":"Jesus F."},{"last_name":"Knopfova","first_name":"Lucia","full_name":"Knopfova, Lucia"},{"full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder","first_name":"Mathias"},{"first_name":"Bruno","last_name":"Luckow","full_name":"Luckow, Bruno"},{"full_name":"Schneider, Stefan W.","last_name":"Schneider","first_name":"Stefan W."},{"last_name":"Borsig","first_name":"Lubor","full_name":"Borsig, Lubor"}],"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"AACR","year":"2019","pmid":1,"date_published":"2019-03-01T00:00:00Z","article_type":"original","page":"783-793","publication":"Molecular Cancer Research","citation":{"chicago":"Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research. AACR, 2019. https://doi.org/10.1158/1541-7786.MCR-18-0530.","short":"M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular Cancer Research 17 (2019) 783–793.","mla":"Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research, vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:10.1158/1541-7786.MCR-18-0530.","ieee":"M. Roblek et al., “CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis,” Molecular Cancer Research, vol. 17, no. 3. AACR, pp. 783–793, 2019.","apa":"Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530","ista":"Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 17(3), 783–793.","ama":"Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","intvolume":" 17","_id":"6190","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis.","lang":"eng"}],"issue":"3","type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies."}],"title":"Why structure matters","ddc":["570"],"status":"public","intvolume":" 8","_id":"6230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"6293","date_created":"2019-04-11T11:43:38Z","date_updated":"2020-07-14T12:47:24Z","checksum":"130d7544b57df4a6787e1263c2d7ea43","file_name":"2019_eLife_Barton.pdf","access_level":"open_access","file_size":298466,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"No","publication":"eLife","citation":{"short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380.","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380."},"date_published":"2019-03-21T00:00:00Z","article_number":"e45380","file_date_updated":"2020-07-14T12:47:24Z","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","year":"2019","date_updated":"2023-08-25T08:59:38Z","date_created":"2019-04-07T21:59:15Z","volume":8,"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"},{"first_name":"Magnus","last_name":"Nordborg","full_name":"Nordborg, Magnus"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","description":"News on IST Homepage","relation":"press_release"}]},"month":"03","publication_identifier":{"eissn":["2050084X"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000461988300001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.45380"},{"page":"804-834","publication":"Annals of Probability","citation":{"ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834.","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","mla":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272.","short":"M. Gerencser, Annals of Probability 47 (2019) 804–834."},"date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Boundary regularity of stochastic PDEs","intvolume":" 47","_id":"6232","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.","lang":"eng"}],"issue":"2","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1705.05364"],"isi":["000459681900005"]},"main_file_link":[{"url":"https://arxiv.org/abs/1705.05364","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/18-AOP1272","month":"03","publication_identifier":{"issn":["00911798"]},"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"year":"2019","date_created":"2019-04-07T21:59:15Z","date_updated":"2023-08-25T08:59:11Z","volume":47,"author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate"}]},{"month":"06","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313x"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000473644100008"],"pmid":["30821050"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.1111/tpj.14301","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:25Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han"},{"first_name":"Petr","last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-25T10:11:03Z","date_created":"2019-04-09T08:46:44Z","volume":98,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"The Plant Journal","citation":{"chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.","apa":"Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301","ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059.","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301"},"article_type":"original","page":"1048-1059","date_published":"2019-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development."}],"issue":"6","_id":"6262","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","ddc":["580"],"status":"public","intvolume":" 98","oa_version":"Published Version","file":[{"file_name":"2019_PlantJournal_Rakusov.pdf","access_level":"open_access","file_size":1383100,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6304","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-15T09:38:43Z","checksum":"ad3b5e270b67ba2a45f894ce3be27920"}]},{"date_published":"2019-05-01T00:00:00Z","page":"47-59","article_type":"original","citation":{"ieee":"H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier, 2019. https://doi.org/10.1016/j.matbio.2018.12.002.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002."},"publication":"Matrix Biology","has_accepted_license":"1","article_processing_charge":"No","day":"01","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2018_MatrixBiology_Davies.pdf","content_type":"application/pdf","file_size":4444339,"creator":"dernst","relation":"main_file","file_id":"7825","checksum":"790878cd78bfc54a147ddcc7c8f286a0","date_updated":"2020-07-14T12:47:27Z","date_created":"2020-05-14T09:02:07Z"}],"title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6297","abstract":[{"text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.matbio.2018.12.002","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000468707600005"]},"publication_identifier":{"issn":["0945-053X"]},"month":"05","volume":"78-79","date_created":"2019-04-11T20:55:01Z","date_updated":"2023-08-25T10:11:28Z","author":[{"last_name":"Davies","first_name":"Heather S.","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S."},{"last_name":"El Amri","first_name":"Nouha","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","first_name":"Liliane","last_name":"Coche-Guérente"},{"first_name":"Claude","last_name":"Verdier","full_name":"Verdier, Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"last_name":"Richter","first_name":"Ralf P.","full_name":"Richter, Ralf P."},{"full_name":"Débarre, Delphine","first_name":"Delphine","last_name":"Débarre"}],"department":[{"_id":"MaLo"}],"publisher":"Elsevier","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:27Z"},{"oa":1,"external_id":{"arxiv":["1810.08426"],"isi":["000468857300025"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.aim.2019.04.031","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10902082"],"issn":["00018708"]},"month":"06","year":"2019","department":[{"_id":"TiBr"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"first_name":"L.Q.","last_name":"Hu","full_name":"Hu, L.Q."}],"volume":349,"date_created":"2019-04-16T09:13:25Z","date_updated":"2023-08-25T10:11:55Z","file_date_updated":"2020-07-14T12:47:27Z","citation":{"ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940.","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.","apa":"Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031","ama":"Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031","chicago":"Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.","mla":"Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp. 920–40, doi:10.1016/j.aim.2019.04.031.","short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940."},"publication":"Advances in Mathematics","page":"920-940","date_published":"2019-06-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6310","intvolume":" 349","status":"public","title":"Counting rational points on biquadratic hypersurfaces","ddc":["512"],"oa_version":"Submitted Version","file":[{"creator":"tbrownin","content_type":"application/pdf","file_size":379158,"access_level":"open_access","file_name":"wliqun.pdf","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-16T09:12:20Z","file_id":"6311","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method.","lang":"eng"}]},{"date_published":"2019-05-01T00:00:00Z","article_type":"letter_note","page":"22-25","publication":"Plant Physiology","citation":{"chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","apa":"Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305","ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp. 22–25, 2019.","ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"Nitrate modulates the differentiation of root distal stem cells","status":"public","intvolume":" 180","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6261","abstract":[{"text":"Nitrate regulation of root stem cell activity is auxin-dependent.","lang":"eng"}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1104/pp.18.01305","quality_controlled":"1","isi":1,"external_id":{"isi":["000466860800010"],"pmid":["30787134"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1104/pp.18.01305","open_access":"1"}],"month":"05","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"date_updated":"2023-08-25T10:10:23Z","date_created":"2019-04-09T08:46:17Z","volume":180,"author":[{"full_name":"Wang, Y","first_name":"Y","last_name":"Wang"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"ASPB","year":"2019","pmid":1},{"publisher":"Springer","department":[{"_id":"LeSa"}],"publication_status":"published","year":"2019","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","date_updated":"2023-08-25T10:14:26Z","date_created":"2019-04-28T21:59:14Z","author":[{"full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov","first_name":"Andrey Alexandrovich"},{"last_name":"Rogov","first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich"},{"full_name":"Sklifas, Alla Nikolaevna","first_name":"Alla Nikolaevna","last_name":"Sklifas"},{"full_name":"Klychnikova, Elena Valerievna","last_name":"Klychnikova","first_name":"Elena Valerievna"},{"first_name":"Markus","last_name":"Hartl","full_name":"Hartl, Markus"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej","last_name":"Charnagalov","full_name":"Charnagalov, Alexej"}],"file_date_updated":"2020-07-14T12:47:28Z","quality_controlled":"1","isi":1,"external_id":{"isi":["000470332600049"]},"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,"language":[{"iso":"eng"}],"doi":"10.1007/s11033-019-04765-z","publication_identifier":{"issn":["03014851"],"eissn":["15734978"]},"month":"04","status":"public","ddc":["570"],"title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6352","file":[{"content_type":"application/pdf","file_size":1948014,"creator":"dernst","access_level":"open_access","file_name":"2019_MolecularBioReport_Temnov.pdf","checksum":"45bf040bbce1cea274f6013fa18ba21b","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T09:52:36Z","relation":"main_file","file_id":"6362"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure."}],"citation":{"apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z","ieee":"A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z."},"publication":"Molecular Biology Reports","date_published":"2019-04-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"12"},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6348","title":"Resonant electro-optic frequency comb","status":"public","intvolume":" 568","abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"issue":"7752","type":"journal_article","date_published":"2019-04-18T00:00:00Z","publication":"Nature","citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381."},"page":"378-381","day":"18","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"date_created":"2019-04-28T21:59:13Z","date_updated":"2023-08-25T10:15:25Z","volume":568,"year":"2019","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","doi":"10.1038/s41586-019-1110-x","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1808.10608"],"isi":["000464950700053"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.10608"}],"quality_controlled":"1","isi":1,"month":"04","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]}},{"abstract":[{"text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6338","intvolume":" 102","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","status":"public","article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2019-04-17T00:00:00Z","citation":{"ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.","apa":"Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019.","ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052","chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.","mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461."},"publication":"Neuron","page":"450-461","article_type":"original","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico"},{"full_name":"Baracskay, Peter","last_name":"Baracskay","first_name":"Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill"},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"volume":102,"date_created":"2019-04-17T08:28:59Z","date_updated":"2023-08-25T10:13:07Z","pmid":1,"year":"2019","department":[{"_id":"JoCs"}],"publisher":"Elsevier","publication_status":"published","month":"04","doi":"10.1016/j.neuron.2019.01.052","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"oa":1,"external_id":{"pmid":["30819547"],"isi":["000465169700017"]},"project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"name":"Interneuro Plasticity During Spatial Learning","call_identifier":"FWF","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5878","title":"State space geometry of the chaotic pilot-wave hydrodynamics","status":"public","intvolume":" 29","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al."}],"issue":"1","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","citation":{"chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.","apa":"Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279","ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279"},"article_type":"original","date_published":"2019-01-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","year":"2019","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"BjHo"}],"author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"first_name":"Marc","last_name":"Fleury","full_name":"Fleury, Marc"}],"related_material":{"link":[{"relation":"erratum","url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157"}]},"date_created":"2019-01-23T08:35:09Z","date_updated":"2023-08-25T10:16:11Z","volume":29,"article_number":"013122","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.09011"}],"oa":1,"external_id":{"isi":["000457409100028"],"arxiv":["1812.09011"]},"isi":1,"quality_controlled":"1","doi":"10.1063/1.5058279","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]}},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","page":"1-9","article_type":"original","citation":{"ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9.","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” Current Opinion in Structural Biology, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018","chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.","mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9."},"publication":"Current Opinion in Structural Biology","issue":"10","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA."}],"type":"journal_article","oa_version":"None","intvolume":" 58","title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","status":"public","_id":"6343","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0959-440X"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2019.03.018","quality_controlled":"1","isi":1,"external_id":{"isi":["000494891800004"]},"volume":58,"date_updated":"2023-08-25T10:13:31Z","date_created":"2019-04-19T11:19:13Z","author":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"department":[{"_id":"FlSc"}],"publisher":"Elsevier","publication_status":"published","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","year":"2019"},{"file_date_updated":"2020-10-08T17:25:45Z","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"first_name":"Alexandre","last_name":"Donzé","full_name":"Donzé, Alexandre"},{"last_name":"Ito","first_name":"Hisahiro","full_name":"Ito, Hisahiro"},{"full_name":"Kapinski, James","first_name":"James","last_name":"Kapinski"}],"date_updated":"2023-08-25T10:19:23Z","date_created":"2019-05-13T08:13:46Z","year":"2019","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","publication_identifier":{"isbn":["9781450362825"]},"month":"04","doi":"10.1145/3302504.3311800","conference":{"end_date":"2019-04-18","start_date":"2019-04-16","location":"Montreal, Canada","name":"HSCC: Hybrid Systems Computation and Control"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000516713900007"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system."}],"type":"conference","oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Ferrere.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1055421,"creator":"dernst","relation":"main_file","file_id":"8633","date_updated":"2020-10-08T17:25:45Z","date_created":"2020-10-08T17:25:45Z","checksum":"b8e967081e051d1c55ca5d18fb187890","success":1}],"_id":"6428","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000"],"status":"public","title":"Interface-aware signal temporal logic","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","date_published":"2019-04-16T00:00:00Z","citation":{"ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800."},"publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","page":"57-66"},{"date_published":"2019-07-01T00:00:00Z","citation":{"short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130."},"publication":"ACM Transactions on Graphics","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"file_name":"2019_ACM_Schreck.pdf","access_level":"open_access","content_type":"application/pdf","file_size":44328918,"creator":"dernst","relation":"main_file","file_id":"6443","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-14T07:03:55Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673"}],"oa_version":"Submitted Version","intvolume":" 38","ddc":["000","005"],"status":"public","title":"Fundamental solutions for water wave animation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6442","issue":"4","abstract":[{"text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3306346.3323002","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000475740600104"]},"oa":1,"month":"07","volume":38,"date_created":"2019-05-14T07:04:06Z","date_updated":"2023-08-25T10:18:46Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","article_number":"130"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6413","status":"public","title":"Phase-field simulation of core-annular pipe flow","intvolume":" 117","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"International Journal of Multiphase Flow","citation":{"ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24."},"article_type":"original","page":"14-24","date_published":"2019-08-01T00:00:00Z","year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"author":[{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"last_name":"Plana","first_name":"Carlos","full_name":"Plana, Carlos"},{"orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"date_updated":"2023-08-25T10:19:55Z","date_created":"2019-05-13T07:58:35Z","volume":117,"month":"08","publication_identifier":{"issn":["03019322"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","language":[{"iso":"eng"}]},{"oa_version":"Published Version","file":[{"date_created":"2019-05-14T08:26:08Z","date_updated":"2020-07-14T12:47:30Z","checksum":"cf3889c8a8a16053dacf9c3776cbe217","file_id":"6445","relation":"main_file","creator":"dernst","file_size":3726017,"content_type":"application/pdf","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6419","intvolume":" 15","ddc":["570"],"status":"public","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","issue":"4","abstract":[{"text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.","lang":"eng"}],"type":"journal_article","date_published":"2019-04-10T00:00:00Z","citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. 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The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6412","ddc":["570"],"status":"public","title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","intvolume":" 10","oa_version":"Published Version","file":[{"checksum":"6550a328335396c856db4cbdda7d2994","date_created":"2019-05-14T08:45:51Z","date_updated":"2020-07-14T12:47:29Z","relation":"main_file","file_id":"6448","file_size":1223647,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf"}],"scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6"},"date_published":"2019-04-29T00:00:00Z"},{"scopus_import":"1","publication_identifier":{"eissn":["22145753"],"issn":["22145745"]},"article_processing_charge":"No","day":"01","month":"06","citation":{"mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.","ama":"Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011"},"external_id":{"isi":["000477666000012"]},"publication":"Current Opinion in Insect Science","page":"63-68","isi":1,"quality_controlled":"1","date_published":"2019-06-01T00:00:00Z","doi":"10.1016/j.cois.2019.03.011","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success."}],"_id":"6415","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SyCr"}],"publisher":"Elsevier","intvolume":" 33","status":"public","title":"Pathogens and disease defense of invasive ants","publication_status":"published","author":[{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"oa_version":"None","volume":33,"date_created":"2019-05-13T07:58:36Z","date_updated":"2023-08-25T10:31:31Z"},{"_id":"9790","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","status":"public","title":"A statistical summary of segment libraries and sequencing results","related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria","full_name":"Pokusaeva, Victoria"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V."},{"full_name":"Espinar, Lorena","last_name":"Espinar","first_name":"Lorena"},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","last_name":"Sarkisyan","first_name":"Karen"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"last_name":"Bogatyreva","first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S."},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov"},{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey"},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"oa_version":"Published Version","date_created":"2021-08-06T08:50:15Z","date_updated":"2023-08-25T10:30:36Z","type":"research_data_reference","citation":{"mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019."},"date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s011","article_processing_charge":"No","day":"10","month":"04"}]