[{"publication_identifier":{"eissn":["15573125"],"issn":["15417786"]},"month":"03","doi":"10.1158/1541-7786.MCR-18-0530","language":[{"iso":"eng"}],"external_id":{"isi":["000460099800012"],"pmid":["30552233"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1158/1541-7786.MCR-18-0530"}],"oa":1,"isi":1,"quality_controlled":"1","author":[{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko","last_name":"Roblek","full_name":"Roblek, Marko"},{"full_name":"Protsyuk, Darya","last_name":"Protsyuk","first_name":"Darya"},{"first_name":"Paul F.","last_name":"Becker","full_name":"Becker, Paul F."},{"full_name":"Stefanescu, Cristina","last_name":"Stefanescu","first_name":"Cristina"},{"last_name":"Gorzelanny","first_name":"Christian","full_name":"Gorzelanny, Christian"},{"last_name":"Glaus Garzon","first_name":"Jesus F.","full_name":"Glaus Garzon, Jesus F."},{"first_name":"Lucia","last_name":"Knopfova","full_name":"Knopfova, Lucia"},{"full_name":"Heikenwalder, Mathias","first_name":"Mathias","last_name":"Heikenwalder"},{"last_name":"Luckow","first_name":"Bruno","full_name":"Luckow, Bruno"},{"last_name":"Schneider","first_name":"Stefan W.","full_name":"Schneider, Stefan W."},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"volume":17,"date_updated":"2023-08-25T08:57:01Z","date_created":"2019-03-31T21:59:12Z","pmid":1,"year":"2019","publisher":"AACR","department":[{"_id":"DaSi"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","citation":{"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.","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","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","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.","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.","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."},"publication":"Molecular Cancer Research","page":"783-793","article_type":"original","issue":"3","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"}],"type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6190","intvolume":" 17","status":"public","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","citation":{"ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. 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.","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019)."},"publication":"eLife","date_published":"2019-03-21T00:00:00Z","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."}],"_id":"6230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 8","ddc":["570"],"status":"public","title":"Why structure matters","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6293","checksum":"130d7544b57df4a6787e1263c2d7ea43","date_updated":"2020-07-14T12:47:24Z","date_created":"2019-04-11T11:43:38Z","access_level":"open_access","file_name":"2019_eLife_Barton.pdf","file_size":298466,"content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"eissn":["2050084X"]},"month":"03","external_id":{"isi":["000461988300001"]},"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,"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.45380","language":[{"iso":"eng"}],"article_number":"e45380","file_date_updated":"2020-07-14T12:47:24Z","year":"2019","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"},{"full_name":"Nordborg, Magnus","first_name":"Magnus","last_name":"Nordborg"}],"volume":8,"date_updated":"2023-08-25T08:59:38Z","date_created":"2019-04-07T21:59:15Z"},{"publication_identifier":{"issn":["00911798"]},"month":"03","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.05364","open_access":"1"}],"external_id":{"arxiv":["1705.05364"],"isi":["000459681900005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/18-AOP1272","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2019","volume":47,"date_updated":"2023-08-25T08:59:11Z","date_created":"2019-04-07T21:59:15Z","author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"804-834","citation":{"short":"M. Gerencser, Annals of Probability 47 (2019) 804–834.","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.","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272","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.","ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834."},"publication":"Annals of Probability","date_published":"2019-03-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","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."}],"intvolume":" 47","title":"Boundary regularity of stochastic PDEs","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6232","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":{"isi":["000473644100008"],"pmid":["30821050"]},"oa":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1111/tpj.14301","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-313x"],"issn":["0960-7412"]},"month":"06","pmid":1,"year":"2019","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","author":[{"last_name":"Rakusová","first_name":"Hana","full_name":"Rakusová, Hana"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"last_name":"Valošek","first_name":"Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"volume":98,"date_updated":"2023-08-25T10:11:03Z","date_created":"2019-04-09T08:46:44Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:25Z","citation":{"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.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","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.","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","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.","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","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."},"publication":"The Plant Journal","page":"1048-1059","article_type":"original","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6262","intvolume":" 98","title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","ddc":["580"],"status":"public","file":[{"file_size":1383100,"content_type":"application/pdf","creator":"dernst","file_name":"2019_PlantJournal_Rakusov.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-15T09:38:43Z","checksum":"ad3b5e270b67ba2a45f894ce3be27920","relation":"main_file","file_id":"6304"}],"oa_version":"Published Version","type":"journal_article","issue":"6","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."}]},{"ddc":["570"],"status":"public","title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6297","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_created":"2020-05-14T09:02:07Z","date_updated":"2020-07-14T12:47:27Z"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"page":"47-59","article_type":"original","citation":{"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","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.","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","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.","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.","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.","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."},"publication":"Matrix Biology","date_published":"2019-05-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01","department":[{"_id":"MaLo"}],"publisher":"Elsevier","publication_status":"published","year":"2019","volume":"78-79","date_updated":"2023-08-25T10:11:28Z","date_created":"2019-04-11T20:55:01Z","author":[{"first_name":"Heather S.","last_name":"Davies","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","last_name":"Baranova","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nouha","last_name":"El Amri","full_name":"El Amri, Nouha"},{"first_name":"Liliane","last_name":"Coche-Guérente","full_name":"Coche-Guérente, Liliane"},{"full_name":"Verdier, Claude","first_name":"Claude","last_name":"Verdier"},{"last_name":"Bureau","first_name":"Lionel","full_name":"Bureau, Lionel"},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."},{"full_name":"Débarre, Delphine","last_name":"Débarre","first_name":"Delphine"}],"file_date_updated":"2020-07-14T12:47:27Z","isi":1,"quality_controlled":"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"},"oa":1,"external_id":{"isi":["000468707600005"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.matbio.2018.12.002","publication_identifier":{"issn":["0945-053X"]},"month":"05"},{"day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-06-20T00:00:00Z","page":"920-940","publication":"Advances in Mathematics","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."},"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"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6311","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","date_created":"2019-04-16T09:12:20Z","date_updated":"2020-07-14T12:47:27Z","access_level":"open_access","file_name":"wliqun.pdf","content_type":"application/pdf","file_size":379158,"creator":"tbrownin"}],"oa_version":"Submitted Version","status":"public","title":"Counting rational points on biquadratic hypersurfaces","ddc":["512"],"intvolume":" 349","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6310","month":"06","publication_identifier":{"eissn":["10902082"],"issn":["00018708"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2019.04.031","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1810.08426"],"isi":["000468857300025"]},"file_date_updated":"2020-07-14T12:47:27Z","date_updated":"2023-08-25T10:11:55Z","date_created":"2019-04-16T09:13:25Z","volume":349,"author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"first_name":"L.Q.","last_name":"Hu","full_name":"Hu, L.Q."}],"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Elsevier","year":"2019"},{"oa":1,"external_id":{"isi":["000466860800010"],"pmid":["30787134"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.18.01305"}],"quality_controlled":"1","isi":1,"doi":"10.1104/pp.18.01305","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"month":"05","pmid":1,"year":"2019","publisher":"ASPB","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"first_name":"Y","last_name":"Wang","full_name":"Wang, Y"},{"first_name":"Z","last_name":"Gong","full_name":"Gong, Z"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"}],"volume":180,"date_created":"2019-04-09T08:46:17Z","date_updated":"2023-08-25T10:10:23Z","citation":{"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.","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.","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","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.","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.","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"},"publication":"Plant Physiology","page":"22-25","article_type":"letter_note","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"6261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 180","status":"public","title":"Nitrate modulates the differentiation of root distal stem cells","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Nitrate regulation of root stem cell activity is auxin-dependent."}]},{"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."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_MolecularBioReport_Temnov.pdf","creator":"dernst","file_size":1948014,"content_type":"application/pdf","file_id":"6362","relation":"main_file","checksum":"45bf040bbce1cea274f6013fa18ba21b","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T09:52:36Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6352","ddc":["570"],"title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","status":"public","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"12","scopus_import":"1","date_published":"2019-04-12T00:00:00Z","citation":{"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.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","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.","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","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.","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."},"publication":"Molecular Biology Reports","file_date_updated":"2020-07-14T12:47:28Z","author":[{"full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov","first_name":"Andrey Alexandrovich"},{"first_name":"Konstantin Arkadevich","last_name":"Rogov","full_name":"Rogov, Konstantin Arkadevich"},{"full_name":"Sklifas, Alla Nikolaevna","last_name":"Sklifas","first_name":"Alla Nikolaevna"},{"last_name":"Klychnikova","first_name":"Elena Valerievna","full_name":"Klychnikova, Elena Valerievna"},{"last_name":"Hartl","first_name":"Markus","full_name":"Hartl, Markus"},{"last_name":"Djinovic-Carugo","first_name":"Kristina","full_name":"Djinovic-Carugo, Kristina"},{"id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej","last_name":"Charnagalov","full_name":"Charnagalov, Alexej"}],"date_updated":"2023-08-25T10:14:26Z","date_created":"2019-04-28T21:59:14Z","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","publisher":"Springer","department":[{"_id":"LeSa"}],"publication_status":"published","publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"month":"04","doi":"10.1007/s11033-019-04765-z","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":{"isi":["000470332600049"]},"isi":1,"quality_controlled":"1"},{"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"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"},{"last_name":"Sedlmeir","first_name":"Florian","full_name":"Sedlmeir, Florian"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"date_updated":"2023-08-25T10:15:25Z","date_created":"2019-04-28T21:59:13Z","volume":568,"oa":1,"external_id":{"arxiv":["1808.10608"],"isi":["000464950700053"]},"main_file_link":[{"url":"https://arxiv.org/abs/1808.10608","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-019-1110-x","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"_id":"6348","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Resonant electro-optic frequency comb","status":"public","intvolume":" 568","oa_version":"Preprint","type":"journal_article","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","publication":"Nature","citation":{"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.","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","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","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.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","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."},"page":"378-381","date_published":"2019-04-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"6338","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","intvolume":" 102","oa_version":"Published Version","scopus_import":"1","day":"17","article_processing_charge":"No","publication":"Neuron","citation":{"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.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.","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.","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.","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","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.","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"},"article_type":"original","page":"450-461","date_published":"2019-04-17T00:00:00Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Elsevier","author":[{"orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella","first_name":"Federico","full_name":"Stella, Federico"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","first_name":"Peter","full_name":"Baracskay, Peter"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/"}]},"date_created":"2019-04-17T08:28:59Z","date_updated":"2023-08-25T10:13:07Z","volume":102,"month":"04","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"external_id":{"pmid":["30819547"],"isi":["000465169700017"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425","name":"Interneuro Plasticity During Spatial Learning","call_identifier":"FWF"}],"doi":"10.1016/j.neuron.2019.01.052","language":[{"iso":"eng"}]},{"department":[{"_id":"BjHo"}],"publisher":"AIP Publishing","publication_status":"published","year":"2019","volume":29,"date_created":"2019-01-23T08:35:09Z","date_updated":"2023-08-25T10:16:11Z","related_material":{"link":[{"relation":"erratum","url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157"}]},"author":[{"first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"},{"first_name":"Marc","last_name":"Fleury","full_name":"Fleury, Marc"}],"article_number":"013122","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1812.09011"],"isi":["000457409100028"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.09011"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.5058279","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"month":"01","intvolume":" 29","title":"State space geometry of the chaotic pilot-wave hydrodynamics","status":"public","_id":"5878","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"1","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."}],"article_type":"original","citation":{"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","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.","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","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.","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).","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."},"publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_published":"2019-01-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22"},{"year":"2019","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Elsevier","author":[{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"date_created":"2019-04-19T11:19:13Z","date_updated":"2023-08-25T10:13:31Z","volume":58,"month":"10","publication_identifier":{"issn":["0959-440X"]},"external_id":{"isi":["000494891800004"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.sbi.2019.03.018","language":[{"iso":"eng"}],"type":"journal_article","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."}],"issue":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6343","status":"public","title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","intvolume":" 58","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Current Opinion in Structural Biology","citation":{"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","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.","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.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.","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."},"article_type":"original","page":"1-9","date_published":"2019-10-01T00:00:00Z"},{"file":[{"relation":"main_file","file_id":"8633","checksum":"b8e967081e051d1c55ca5d18fb187890","success":1,"date_created":"2020-10-08T17:25:45Z","date_updated":"2020-10-08T17:25:45Z","access_level":"open_access","file_name":"2019_ACM_Ferrere.pdf","content_type":"application/pdf","file_size":1055421,"creator":"dernst"}],"oa_version":"Submitted Version","_id":"6428","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Interface-aware signal temporal logic","ddc":["000"],"status":"public","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","date_published":"2019-04-16T00:00:00Z","citation":{"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.","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.","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.","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","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.","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.","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"},"publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","page":"57-66","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"full_name":"Ito, Hisahiro","first_name":"Hisahiro","last_name":"Ito"},{"last_name":"Kapinski","first_name":"James","full_name":"Kapinski, James"}],"date_created":"2019-05-13T08:13:46Z","date_updated":"2023-08-25T10:19:23Z","year":"2019","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","file_date_updated":"2020-10-08T17:25:45Z","doi":"10.1145/3302504.3311800","conference":{"name":"HSCC: Hybrid Systems Computation and Control","start_date":"2019-04-16","location":"Montreal, Canada","end_date":"2019-04-18"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000516713900007"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781450362825"]},"month":"04"},{"oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Schreck.pdf","access_level":"open_access","file_size":44328918,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6443","date_created":"2019-05-14T07:03:55Z","date_updated":"2020-07-14T12:47:30Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673"}],"status":"public","ddc":["000","005"],"title":"Fundamental solutions for water wave animation","intvolume":" 38","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6442","abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","date_published":"2019-07-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"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","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","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","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.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","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."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_created":"2019-05-14T07:04:06Z","date_updated":"2023-08-25T10:18:46Z","volume":38,"author":[{"last_name":"Schreck","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille"},{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"year":"2019","file_date_updated":"2020-07-14T12:47:30Z","ec_funded":1,"article_number":"130","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3306346.3323002","isi":1,"quality_controlled":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["000475740600104"]},"month":"07"},{"publisher":"Elsevier","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":117,"date_created":"2019-05-13T07:58:35Z","date_updated":"2023-08-25T10:19:55Z","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"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"publication_identifier":{"issn":["03019322"]},"month":"08","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","type":"journal_article","abstract":[{"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.","lang":"eng"}],"intvolume":" 117","title":"Phase-field simulation of core-annular pipe flow","status":"public","_id":"6413","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"14-24","article_type":"original","citation":{"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","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","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.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","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.","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."},"publication":"International Journal of Multiphase Flow","date_published":"2019-08-01T00:00:00Z"},{"date_published":"2019-04-10T00:00:00Z","citation":{"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.","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.","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","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.","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. PLoS Genetics. 15(4), e1008079.","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"},"publication":"PLoS Genetics","has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1","file":[{"checksum":"cf3889c8a8a16053dacf9c3776cbe217","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-14T08:26:08Z","relation":"main_file","file_id":"6445","content_type":"application/pdf","file_size":3726017,"creator":"dernst","access_level":"open_access","file_name":"2019_PLOSGenetics_Pokusaeva.pdf"}],"oa_version":"Published Version","intvolume":" 15","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6419","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","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008079","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000466866000029"]},"oa":1,"publication_identifier":{"eissn":["15537404"]},"month":"04","volume":15,"date_created":"2019-05-13T07:58:38Z","date_updated":"2023-08-25T10:30:37Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9789"},{"id":"9790","status":"public","relation":"research_data"},{"id":"9797","status":"public","relation":"research_data"}]},"author":[{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria"},{"last_name":"Usmanova","first_name":"Dinara R.","full_name":"Usmanova, Dinara R."},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"last_name":"Espinar","first_name":"Lorena","full_name":"Espinar, 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."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry"},{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov"},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, 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."},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","article_number":"e1008079"},{"article_number":"1931","file_date_updated":"2020-07-14T12:47:29Z","publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","year":"2019","date_created":"2019-05-13T07:58:35Z","date_updated":"2023-08-25T10:31:56Z","volume":10,"author":[{"last_name":"Moussa","first_name":"Hagar F.","full_name":"Moussa, Hagar F."},{"full_name":"Bsteh, Daniel","last_name":"Bsteh","first_name":"Daniel"},{"full_name":"Yelagandula, Ramesh","first_name":"Ramesh","last_name":"Yelagandula"},{"full_name":"Pribitzer, Carina","first_name":"Carina","last_name":"Pribitzer"},{"first_name":"Karin","last_name":"Stecher","full_name":"Stecher, Karin"},{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bartalska","full_name":"Bartalska, Katarina"},{"full_name":"Michetti, Luca","first_name":"Luca","last_name":"Michetti"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Jorge A.","last_name":"Zepeda-Martinez","full_name":"Zepeda-Martinez, Jorge A."},{"first_name":"Ulrich","last_name":"Elling","full_name":"Elling, Ulrich"},{"full_name":"Stuckey, Jacob I.","last_name":"Stuckey","first_name":"Jacob I."},{"full_name":"James, Lindsey I.","first_name":"Lindsey I.","last_name":"James"},{"full_name":"Frye, Stephen V.","last_name":"Frye","first_name":"Stephen V."},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"month":"04","publication_identifier":{"eissn":["20411723"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000466118700002"]},"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":"10.1038/s41467-019-09628-6","type":"journal_article","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. 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","status":"public","title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","ddc":["570"],"intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6412","file":[{"content_type":"application/pdf","file_size":1223647,"creator":"dernst","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf","checksum":"6550a328335396c856db4cbdda7d2994","date_created":"2019-05-14T08:45:51Z","date_updated":"2020-07-14T12:47:29Z","relation":"main_file","file_id":"6448"}],"oa_version":"Published Version","scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"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.","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","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","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."},"date_published":"2019-04-29T00:00:00Z"},{"author":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"oa_version":"None","volume":33,"date_created":"2019-05-13T07:58:36Z","date_updated":"2023-08-25T10:31:31Z","_id":"6415","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SyCr"}],"publisher":"Elsevier","intvolume":" 33","status":"public","publication_status":"published","title":"Pathogens and disease defense of invasive ants","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."}],"type":"journal_article","doi":"10.1016/j.cois.2019.03.011","date_published":"2019-06-01T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000477666000012"]},"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. 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Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010."},"date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s010"},{"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"month":"07","project":[{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491468000036"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-25540-4_36","conference":{"name":"CAV: Computer Aided Verification","end_date":"2019-07-18","start_date":"2019-07-13","location":"New York, NY, United States"},"file_date_updated":"2020-07-14T12:47:31Z","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","year":"2019","volume":11561,"date_created":"2019-05-16T11:22:30Z","date_updated":"2023-08-25T10:33:27Z","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Konighofer, Bettina","last_name":"Konighofer","first_name":"Bettina"},{"first_name":"Stefan","last_name":"Pranger","full_name":"Pranger, Stefan"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","page":"630-649","citation":{"chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36.","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36"},"publication":"31st International Conference on Computer-Aided Verification","date_published":"2019-07-12T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles."}],"intvolume":" 11561","title":"Run-time optimization for learned controllers through quantitative games","status":"public","ddc":["000"],"_id":"6462","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":659766,"content_type":"application/pdf","creator":"dernst","file_name":"2019_CAV_Avni.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-08-14T09:35:24Z","checksum":"c231579f2485c6fd4df17c9443a4d80b","relation":"main_file","file_id":"6816"}],"oa_version":"Published Version"},{"month":"05","publication_identifier":{"issn":["1539-0756"],"eissn":["0034-6861"]},"doi":"10.1103/revmodphys.91.021001","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:31Z","article_number":"021001","author":[{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"first_name":"Ehud","last_name":"Altman","full_name":"Altman, Ehud"},{"last_name":"Bloch","first_name":"Immanuel","full_name":"Bloch, Immanuel"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"date_created":"2019-05-23T07:38:43Z","date_updated":"2023-08-25T10:37:56Z","volume":91,"year":"2019","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-05-22T00:00:00Z","publication":"Reviews of Modern Physics","citation":{"ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001","ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.","apa":"Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001."},"article_type":"original","abstract":[{"lang":"eng","text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions."}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6478","relation":"main_file","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-23T07:39:05Z","access_level":"open_access","file_name":"RevModPhys.91.021001.pdf","creator":"mserbyn","file_size":1695677,"content_type":"application/pdf"}],"_id":"6477","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Colloquium: Many-body localization, thermalization, and entanglement","ddc":["530"],"intvolume":" 91"},{"date_published":"2019-04-01T00:00:00Z","page":"1579-1581","citation":{"chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048"},"publication":"Molecular ecology","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"6472","relation":"main_file","date_created":"2019-05-20T11:49:06Z","date_updated":"2020-07-14T12:47:31Z","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","file_name":"2019_MolecularEcology_Field.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":367711}],"intvolume":" 28","title":"Breaking down barriers in morning glories","status":"public","ddc":["580","576"],"_id":"6466","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/mec.15048","isi":1,"quality_controlled":"1","external_id":{"isi":["000474808300001"]},"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,"publication_identifier":{"eissn":["1365294X"]},"month":"04","volume":28,"date_created":"2019-05-19T21:59:15Z","date_updated":"2023-08-25T10:37:30Z","author":[{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:31Z"},{"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-023-36111-0"}]},"author":[{"last_name":"Chassin","first_name":"Hélène","full_name":"Chassin, Hélène"},{"last_name":"Müller","first_name":"Marius","full_name":"Müller, Marius"},{"first_name":"Marcel","last_name":"Tigges","full_name":"Tigges, Marcel"},{"full_name":"Scheller, Leo","last_name":"Scheller","first_name":"Leo"},{"full_name":"Lang, Moritz","first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Fussenegger","full_name":"Fussenegger, Martin"}],"volume":10,"date_updated":"2023-08-25T10:33:51Z","date_created":"2019-05-19T21:59:14Z","year":"2019","department":[{"_id":"CaGu"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:47:31Z","article_number":"2013","doi":"10.1038/s41467-019-09974-5","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":{"isi":["000466338600006"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"month":"05","file":[{"date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-20T07:33:54Z","checksum":"e214d3e4f8c81e35981583c4569b51b8","relation":"main_file","file_id":"6471","file_size":1191827,"content_type":"application/pdf","creator":"dernst","file_name":"2019_NatureComm_Chassin.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6465","intvolume":" 10","status":"public","title":"A modular degron library for synthetic circuits in mammalian cells","ddc":["570"],"issue":"1","abstract":[{"text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.","lang":"eng"}],"type":"journal_article","date_published":"2019-05-01T00:00:00Z","citation":{"ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5","ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5.","chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2018.0881","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"oa":1,"ec_funded":1,"article_number":"0881","volume":15,"date_updated":"2023-08-25T10:34:41Z","date_created":"2019-05-19T21:59:15Z","related_material":{"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}],"record":[{"relation":"research_data","status":"public","id":"9798"},{"id":"9799","status":"public","relation":"research_data"}]},"author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-04-03T00:00:00Z","article_type":"original","citation":{"ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019)."},"publication":"Biology Letters","issue":"4","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 15","title":"The distribution of epistasis on simple fitness landscapes","status":"public","_id":"6467","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"author":[{"last_name":"Éltes","first_name":"Tímea","full_name":"Éltes, Tímea"},{"first_name":"Miklos","last_name":"Szoboszlay","full_name":"Szoboszlay, Miklos"},{"first_name":"Margit Katalin","last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9500-8758","full_name":"Szigeti, Margit Katalin"},{"full_name":"Nusser, Zoltan","last_name":"Nusser","first_name":"Zoltan"}],"date_created":"2019-05-19T21:59:17Z","date_updated":"2023-08-25T10:34:15Z","volume":597,"year":"2019","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"GaNo"}],"month":"06","publication_identifier":{"eissn":["14697793"],"issn":["00223751"]},"doi":"10.1113/JP277681","language":[{"iso":"eng"}],"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1113/JP277681"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6470","status":"public","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","intvolume":" 597","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Journal of Physiology","citation":{"short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947."},"article_type":"original","page":"2925–2947"},{"date_published":"2019-07-12T00:00:00Z","publication":"31st International Conference on Computer-Aided Verification","citation":{"ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314."},"page":"297-314","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Synthesis","Linear hybrid automaton","Membership"],"file":[{"checksum":"1f1d61b83a151031745ef70a501da3d6","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-08-14T11:05:30Z","file_id":"6817","relation":"main_file","creator":"dernst","file_size":674795,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_CAV_GarciaSoto.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6493","title":"Membership-based synthesis of linear hybrid automata","ddc":["000"],"status":"public","intvolume":" 11561","abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"conference":{"name":"CAV: Computer-Aided Verification","end_date":"2019-07-18","location":"New York City, NY, USA","start_date":"2019-07-15"},"doi":"10.1007/978-3-030-25540-4_16","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":{"isi":["000491468000016"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"07","publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"author":[{"full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto","first_name":"Miriam","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"},{"id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","first_name":"Luka","last_name":"Zeleznik","full_name":"Zeleznik, Luka"}],"date_created":"2019-05-27T07:09:53Z","date_updated":"2023-08-25T10:40:41Z","volume":11561,"year":"2019","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:47:32Z","ec_funded":1},{"month":"02","day":"01","publication_identifier":{"isbn":["9781450362252"]},"article_processing_charge":"No","publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418.","ama":"Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000.","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019."},"external_id":{"isi":["000587604600044"]},"isi":1,"quality_controlled":"1","page":"417-418","conference":{"location":"Washington, NY, United States","start_date":"2019-02-16","end_date":"2019-02-20","name":"PPoPP: Principles and Practice of Parallel Programming"},"date_published":"2019-02-01T00:00:00Z","doi":"10.1145/3293883.3297000","language":[{"iso":"eng"}],"type":"conference_poster","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.","lang":"eng"}],"_id":"6485","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","publication_status":"published","status":"public","title":"Lock-free channels for programming via communicating sequential processes","publisher":"ACM Press","department":[{"_id":"DaAl"}],"author":[{"last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"date_created":"2019-05-24T10:09:12Z","date_updated":"2023-08-25T10:41:20Z","oa_version":"None"},{"file":[{"file_name":"2019_NewPhytologist_Zhang_accepted.pdf","access_level":"open_access","file_size":1099061,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8661","date_updated":"2020-10-14T08:59:33Z","date_created":"2020-10-14T08:59:33Z","checksum":"6488243334538f5c39099a701cbf76b9","success":1}],"oa_version":"Submitted Version","title":"Auxin-mediated statolith production for root gravitropism","ddc":["580"],"status":"public","intvolume":" 224","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6504","abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"issue":"2","type":"journal_article","date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"761-774","publication":"New Phytologist","citation":{"ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-28T08:40:13Z","date_created":"2019-05-28T14:33:26Z","volume":224,"author":[{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"He, P","last_name":"He","first_name":"P"},{"last_name":"Ma","first_name":"X","full_name":"Ma, X"},{"last_name":"Yang","first_name":"Z","full_name":"Yang, Z"},{"first_name":"C","last_name":"Pang","full_name":"Pang, C"},{"last_name":"Yu","first_name":"J","full_name":"Yu, J"},{"first_name":"G","last_name":"Wang","full_name":"Wang, G"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Xiao","first_name":"G","full_name":"Xiao, G"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","year":"2019","pmid":1,"file_date_updated":"2020-10-14T08:59:33Z","language":[{"iso":"eng"}],"doi":"10.1111/nph.15932","isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["31111487"],"isi":["000487184200024"]},"month":"10","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]}},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y."},"publication":"Nature Microbiology","page":"1221–1230","article_type":"original","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6506","intvolume":" 4","status":"public","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","oa_version":"Preprint","publication_identifier":{"issn":["2058-5276"]},"month":"07","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"external_id":{"isi":["000480348200017"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41564-019-0412-y","language":[{"iso":"eng"}],"year":"2019","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","last_name":"Davidi","first_name":"Dan"},{"first_name":"Elisa","last_name":"Korenblum","full_name":"Korenblum, Elisa"},{"last_name":"Elazar","first_name":"Assaf","full_name":"Elazar, Assaf"},{"id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Putintseva","full_name":"Putintseva, Ekaterina"},{"full_name":"Aharoni, Asaph","last_name":"Aharoni","first_name":"Asaph"},{"full_name":"Tawfik, Dan S.","first_name":"Dan S.","last_name":"Tawfik"}],"volume":4,"date_updated":"2023-08-28T08:39:47Z","date_created":"2019-05-29T13:03:30Z"},{"author":[{"full_name":"Maes, Margaret E","first_name":"Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","first_name":"Gloria","full_name":"Colombo, Gloria"},{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","first_name":"Rouven"},{"full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"}],"date_created":"2019-06-05T13:16:24Z","date_updated":"2023-08-28T09:30:57Z","volume":707,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"134310","doi":"10.1016/j.neulet.2019.134310","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"},"external_id":{"isi":["000486094600037"],"pmid":["31158432"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571"},{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"month":"08","publication_identifier":{"issn":["0304-3940"]},"file":[{"access_level":"open_access","file_name":"2019_Neuroscience_Maes.pdf","content_type":"application/pdf","file_size":1779287,"creator":"dernst","relation":"main_file","file_id":"6551","checksum":"553c9dbd39727fbed55ee991c51ca4d1","date_created":"2019-06-08T11:44:20Z","date_updated":"2020-07-14T12:47:33Z"}],"oa_version":"Published Version","_id":"6521","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","ddc":["570"],"intvolume":" 707","abstract":[{"lang":"eng","text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies."}],"type":"journal_article","date_published":"2019-08-10T00:00:00Z","publication":"Neuroscience Letters","citation":{"apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310."},"article_type":"original","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"oa_version":"Submitted Version","_id":"6513","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Tracing the origin of adult intestinal stem cells","intvolume":" 570","abstract":[{"text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property.","lang":"eng"}],"type":"journal_article","date_published":"2019-06-06T00:00:00Z","publication":"Nature","citation":{"ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5."},"article_type":"original","page":"107-111","day":"06","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Guiu, Jordi","last_name":"Guiu","first_name":"Jordi"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Yui, Shiro","last_name":"Yui","first_name":"Shiro"},{"last_name":"Demharter","first_name":"Samuel","full_name":"Demharter, Samuel"},{"first_name":"Svetlana","last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana"},{"full_name":"Maimets, Martti","first_name":"Martti","last_name":"Maimets"},{"first_name":"Anne","last_name":"Jørgensen","full_name":"Jørgensen, Anne"},{"full_name":"Perlman, Signe","first_name":"Signe","last_name":"Perlman"},{"last_name":"Lundvall","first_name":"Lene","full_name":"Lundvall, Lene"},{"full_name":"Mamsen, Linn Salto","last_name":"Mamsen","first_name":"Linn Salto"},{"first_name":"Agnete","last_name":"Larsen","full_name":"Larsen, Agnete"},{"full_name":"Olesen, Rasmus H.","first_name":"Rasmus H.","last_name":"Olesen"},{"full_name":"Andersen, Claus Yding","last_name":"Andersen","first_name":"Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","first_name":"Lea Langhoff","last_name":"Thuesen"},{"last_name":"Hare","first_name":"Kristine Juul","full_name":"Hare, Kristine Juul"},{"full_name":"Pers, Tune H.","last_name":"Pers","first_name":"Tune H."},{"first_name":"Konstantin","last_name":"Khodosevich","full_name":"Khodosevich, Konstantin"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"date_created":"2019-06-02T21:59:14Z","date_updated":"2023-08-28T09:30:23Z","volume":570,"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"doi":"10.1038/s41586-019-1212-5","language":[{"iso":"eng"}],"external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"isi":1,"quality_controlled":"1","month":"06","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]}},{"publication":"Journal of Molecular Biology","citation":{"ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033.","short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033."},"article_type":"original","page":"3046-3055","date_published":"2019-08-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","_id":"6564","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","status":"public","intvolume":" 431","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology."}],"issue":"17","oa":1,"main_file_link":[{"url":"http://www.biorxiv.org/content/10.1101/583369v1","open_access":"1"}],"external_id":{"isi":["000482872100002"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.jmb.2019.05.033","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["00222836"],"eissn":["10898638"]},"year":"2019","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Elsevier","author":[{"last_name":"Tichy","first_name":"Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tichy, Alexandra-Madelaine"},{"first_name":"Elliot J.","last_name":"Gerrard","full_name":"Gerrard, Elliot J."},{"first_name":"Julien M.D.","last_name":"Legrand","full_name":"Legrand, Julien M.D."},{"full_name":"Hobbs, Robin M.","last_name":"Hobbs","first_name":"Robin M."},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"date_created":"2019-06-16T21:59:14Z","date_updated":"2023-08-28T09:39:22Z","volume":431},{"publication_identifier":{"issn":["09609822"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2019.03.035","quality_controlled":"1","isi":1,"external_id":{"pmid":["31163158"],"isi":["000470902000023"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2019.03.035","open_access":"1"}],"oa":1,"volume":29,"date_updated":"2023-08-28T09:38:00Z","date_created":"2019-06-09T21:59:10Z","author":[{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"publisher":"Elsevier","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-06-03T00:00:00Z","page":"R458-R463","article_type":"original","citation":{"chicago":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.","short":"S. Cremer, Current Biology 29 (2019) R458–R463.","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.","ieee":"S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","apa":"Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035","ama":"Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035"},"publication":"Current Biology","issue":"11","abstract":[{"text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). ","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 29","status":"public","title":"Social immunity in insects","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6552"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N)."}],"issue":"3","status":"public","title":"Local single ring theorem on optimal scale","intvolume":" 47","_id":"6511","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","page":"1270-1334","publication":"Annals of Probability","citation":{"ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284.","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284."},"date_published":"2019-05-01T00:00:00Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"year":"2019","date_updated":"2023-08-28T09:32:29Z","date_created":"2019-06-02T21:59:13Z","volume":47,"author":[{"full_name":"Bao, Zhigang","first_name":"Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","first_name":"Kevin"}],"month":"05","publication_identifier":{"issn":["00911798"]},"quality_controlled":"1","isi":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.05920","open_access":"1"}],"external_id":{"arxiv":["1612.05920"],"isi":["000466616100003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/18-AOP1284"},{"page":"99-105","article_type":"original","citation":{"ama":"Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008","ieee":"E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019.","apa":"Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008","ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 99–105, doi:10.1016/j.ceb.2019.04.008.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008."},"publication":"Current Opinion in Cell Biology","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 60","status":"public","title":"Multiscale dynamics of branching morphogenesis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6559","oa_version":"None","type":"journal_article","abstract":[{"text":"Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.","lang":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["31181348"],"isi":["000486545800014"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.ceb.2019.04.008","publication_identifier":{"eissn":["18790410"],"issn":["09550674"]},"month":"10","publisher":"Elsevier","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2019","volume":60,"date_created":"2019-06-16T21:59:12Z","date_updated":"2023-08-28T09:38:57Z","author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."}]},{"doi":"10.1021/acsnano.9b00346","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31185159"],"isi":["000473248300043"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"06","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"author":[{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Dobrozhan, Oleksandr","first_name":"Oleksandr","last_name":"Dobrozhan"},{"first_name":"Olga","last_name":"Nazarenko","full_name":"Nazarenko, Olga"},{"last_name":"Mata","first_name":"María de la","full_name":"Mata, María de la"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"full_name":"Kovalenko, Maksym V.","first_name":"Maksym V.","last_name":"Kovalenko"}],"date_updated":"2023-08-28T12:20:53Z","date_created":"2019-06-18T13:54:34Z","volume":13,"year":"2019","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"date_published":"2019-06-25T00:00:00Z","publication":"ACS Nano","citation":{"ama":"Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346","apa":"Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., … Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b00346","ieee":"M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks,” ACS Nano, vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019.","ista":"Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la, Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 13(6), 6572–6580.","short":"M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580.","mla":"Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano, vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346.","chicago":"Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical Society, 2019. https://doi.org/10.1021/acsnano.9b00346."},"article_type":"original","page":"6572-6580","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","keyword":["colloidal nanoparticles","asymmetric nanoparticles","inorganic ligands","heterostructures","catalyst assisted growth","nanocomposites","thermoelectrics"],"file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2019-07-16T14:17:09Z","file_id":"6644","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":8628690,"access_level":"open_access","file_name":"2019_ACSNano_Ibanez.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6566","title":"Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks","ddc":["540"],"status":"public","intvolume":" 13","abstract":[{"text":"Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K.","lang":"eng"}],"issue":"6","type":"journal_article"},{"external_id":{"isi":["000472597400042"]},"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,"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-019-45579-0","language":[{"iso":"eng"}],"month":"06","year":"2019","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"PreCl"}],"author":[{"last_name":"Nguyen","first_name":"Chi Huu","full_name":"Nguyen, Chi Huu"},{"full_name":"Glüxam, Tobias","first_name":"Tobias","last_name":"Glüxam"},{"full_name":"Schlerka, Angela","last_name":"Schlerka","first_name":"Angela"},{"full_name":"Bauer, Katharina","id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","last_name":"Bauer"},{"last_name":"Grandits","first_name":"Alexander M.","full_name":"Grandits, Alexander M."},{"full_name":"Hackl, Hubert","last_name":"Hackl","first_name":"Hubert"},{"first_name":"Oliver","last_name":"Dovey","full_name":"Dovey, Oliver"},{"full_name":"Zöchbauer-Müller, Sabine","first_name":"Sabine","last_name":"Zöchbauer-Müller"},{"last_name":"Cooper","first_name":"Jonathan L.","full_name":"Cooper, Jonathan L."},{"first_name":"George S.","last_name":"Vassiliou","full_name":"Vassiliou, George S."},{"full_name":"Stoiber, Dagmar","last_name":"Stoiber","first_name":"Dagmar"},{"last_name":"Wieser","first_name":"Rotraud","full_name":"Wieser, Rotraud"},{"full_name":"Heller, Gerwin","last_name":"Heller","first_name":"Gerwin"}],"date_updated":"2023-08-28T12:26:51Z","date_created":"2019-07-07T21:59:19Z","volume":9,"article_number":"9139","file_date_updated":"2020-07-14T12:47:34Z","publication":"Scientific Reports","citation":{"short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019).","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0.","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0","apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0","ieee":"C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139."},"date_published":"2019-06-24T00:00:00Z","scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","_id":"6607","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","ddc":["576"],"status":"public","intvolume":" 9","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":2017352,"file_name":"nature_2019_Nguyen.pdf","access_level":"open_access","date_created":"2019-07-08T15:15:28Z","date_updated":"2020-07-14T12:47:34Z","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","file_id":"6623","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically.","lang":"eng"}],"issue":"1"},{"publication":"Nature","citation":{"ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. Nature. 2019;570:480-483. doi:10.1038/s41586-019-1320-2","ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","ieee":"S. Barzanjeh et al., “Stationary entangled radiation from micromechanical motion,” Nature, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., & Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-019-1320-2","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” Nature, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:10.1038/s41586-019-1320-2.","short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483.","chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” Nature. Nature Publishing Group, 2019. https://doi.org/10.1038/s41586-019-1320-2."},"page":"480-483","date_published":"2019-06-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","_id":"6609","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Stationary entangled radiation from micromechanical motion","status":"public","intvolume":" 570","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons."}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.05865"}],"external_id":{"isi":["000472860000042"],"arxiv":["1809.05865"]},"quality_controlled":"1","isi":1,"project":[{"name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"doi":"10.1038/s41586-019-1320-2","acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"month":"06","year":"2019","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoFi"}],"author":[{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias","full_name":"Wulf, Matthias"},{"last_name":"Lewis","first_name":"Dylan","full_name":"Lewis, Dylan"},{"full_name":"Arnold, Georg M","first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"date_created":"2019-07-07T21:59:20Z","date_updated":"2023-08-28T12:29:56Z","volume":570,"ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.1007/s00025-019-1061-4","quality_controlled":"1","isi":1,"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"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":["000473237500002"],"arxiv":["2101.09068"]},"oa":1,"month":"12","publication_identifier":{"issn":["1422-6383"],"eissn":["1420-9012"]},"date_updated":"2023-08-28T12:26:22Z","date_created":"2019-06-29T10:11:30Z","volume":74,"author":[{"orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini","full_name":"Shehu, Yekini"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"VlKo"}],"year":"2019","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"article_number":"138","date_published":"2019-12-01T00:00:00Z","article_type":"original","publication":"Results in Mathematics","citation":{"mla":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics, vol. 74, no. 4, 138, Springer, 2019, doi:10.1007/s00025-019-1061-4.","short":"Y. Shehu, Results in Mathematics 74 (2019).","chicago":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics. Springer, 2019. https://doi.org/10.1007/s00025-019-1061-4.","ama":"Shehu Y. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 2019;74(4). doi:10.1007/s00025-019-1061-4","ista":"Shehu Y. 2019. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138.","ieee":"Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces,” Results in Mathematics, vol. 74, no. 4. Springer, 2019.","apa":"Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. Springer. https://doi.org/10.1007/s00025-019-1061-4"},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","file":[{"file_name":"Springer_2019_Shehu.pdf","access_level":"open_access","creator":"kschuh","file_size":466942,"content_type":"application/pdf","file_id":"6605","relation":"main_file","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-03T15:20:40Z","checksum":"c6d18cb1e16fc0c36a0e0f30b4ebbc2d"}],"oa_version":"Published Version","title":"Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces","status":"public","ddc":["000"],"intvolume":" 74","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6596","abstract":[{"text":"It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper.","lang":"eng"}],"issue":"4","type":"journal_article"},{"publication_identifier":{"issn":["00928674"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2019.05.052","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"external_id":{"pmid":["31251912"],"isi":["000473002700005"]},"ec_funded":1,"volume":178,"date_created":"2019-06-30T21:59:11Z","date_updated":"2023-08-28T12:25:21Z","author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","day":"27","scopus_import":"1","date_published":"2019-07-27T00:00:00Z","page":"12-25","article_type":"review","citation":{"ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052."},"publication":"Cell","issue":"1","abstract":[{"lang":"eng","text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 178","status":"public","title":"Mechanochemical feedback loops in development and disease","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6601"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","page":"635–726","article_type":"original","citation":{"ama":"Fischer JL. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 2019;234(2):635–726. doi:10.1007/s00205-019-01400-w","apa":"Fischer, J. L. (2019). The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w","ieee":"J. L. Fischer, “The choice of representative volumes in the approximation of effective properties of random materials,” Archive for Rational Mechanics and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019.","ista":"Fischer JL. 2019. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 234(2), 635–726.","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726.","mla":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w.","chicago":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w."},"publication":"Archive for Rational Mechanics and Analysis","date_published":"2019-11-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably."}],"intvolume":" 234","status":"public","title":"The choice of representative volumes in the approximation of effective properties of random materials","ddc":["500"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6617","file":[{"creator":"kschuh","file_size":1377659,"content_type":"application/pdf","access_level":"open_access","file_name":"Springer_2019_Fischer.pdf","checksum":"4cff75fa6addb0770991ad9c474ab404","date_created":"2019-07-08T15:56:47Z","date_updated":"2020-07-14T12:47:34Z","file_id":"6626","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"month":"11","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000482386000006"],"arxiv":["1807.00834"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00205-019-01400-w","file_date_updated":"2020-07-14T12:47:34Z","publisher":"Springer","department":[{"_id":"JuFi"}],"publication_status":"published","year":"2019","volume":234,"date_updated":"2023-08-28T12:31:21Z","date_created":"2019-07-07T21:59:23Z","author":[{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer"}]},{"type":"journal_article","issue":"6","abstract":[{"text":"Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.","lang":"eng"}],"_id":"6611","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","title":"PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton","ddc":["580"],"file":[{"creator":"kschuh","file_size":1066773,"content_type":"application/pdf","file_name":"biomolecules-2019-Matous.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:46:32Z","checksum":"1ce1bd36038fe5381057a1bcc6760083","file_id":"6625","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","citation":{"ista":"Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. MDPI. https://doi.org/10.3390/biom9060222","ieee":"M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6. MDPI, 2019.","ama":"Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules. MDPI, 2019. https://doi.org/10.3390/biom9060222.","mla":"Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019, doi:10.3390/biom9060222.","short":"M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019)."},"publication":"Biomolecules","date_published":"2019-06-07T00:00:00Z","article_number":"222","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","pmid":1,"year":"2019","publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"volume":9,"date_created":"2019-07-07T21:59:21Z","date_updated":"2023-08-28T12:30:24Z","month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000475301500018"],"pmid":["31181636"]},"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.3390/biom9060222","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}]},{"abstract":[{"lang":"eng","text":"This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures.\r\n"}],"issue":"12","type":"journal_article","oa_version":"Preprint","_id":"6620","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"On a certain non-split cubic surface","intvolume":" 62","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","publication":"Science China Mathematics","citation":{"ama":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8","ista":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split cubic surface. Science China Mathematics. 62(12), 2435–2446.","ieee":"R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer, pp. 2435–2446, 2019.","apa":"De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019). On a certain non-split cubic surface. Science China Mathematics. Springer. https://doi.org/10.1007/s11425-018-9543-8","mla":"De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8.","short":"R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China Mathematics 62 (2019) 2435–2446.","chicago":"De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics. Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8."},"article_type":"original","page":"2435–2446","author":[{"full_name":"De La Bretèche, Régis","last_name":"De La Bretèche","first_name":"Régis"},{"full_name":"Destagnol, Kevin N","id":"44DDECBC-F248-11E8-B48F-1D18A9856A87","last_name":"Destagnol","first_name":"Kevin N"},{"first_name":"Jianya","last_name":"Liu","full_name":"Liu, Jianya"},{"last_name":"Wu","first_name":"Jie","full_name":"Wu, Jie"},{"first_name":"Yongqiang","last_name":"Zhao","full_name":"Zhao, Yongqiang"}],"date_updated":"2023-08-28T12:32:20Z","date_created":"2019-07-07T21:59:25Z","volume":62,"year":"2019","publication_status":"published","publisher":"Springer","department":[{"_id":"TiBr"}],"month":"12","publication_identifier":{"issn":["16747283"]},"doi":"10.1007/s11425-018-9543-8","language":[{"iso":"eng"}],"external_id":{"isi":["000509102200001"],"arxiv":["1709.09476"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09476"}],"quality_controlled":"1","isi":1},{"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2019","acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","date_created":"2019-07-14T21:59:20Z","date_updated":"2023-08-29T06:31:14Z","volume":73,"author":[{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"last_name":"Krejca","first_name":"Martin ","full_name":"Krejca, Martin "},{"full_name":"Lehre, Per Kristian","last_name":"Lehre","first_name":"Per Kristian"},{"first_name":"Timo","last_name":"Kötzing","full_name":"Kötzing, Timo"}],"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"},{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000474031600001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.13784","month":"07","ddc":["576"],"title":"Surfing on the seascape: Adaptation in a changing environment","status":"public","intvolume":" 73","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6637","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-16T06:08:31Z","checksum":"9831ca65def2d62498c7b08338b6d237","relation":"main_file","file_id":"6643","content_type":"application/pdf","file_size":815416,"creator":"apreinsp","file_name":"2019_Evolution_TrubenovaBarbora.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"issue":"7","article_type":"original","page":"1356-1374","publication":"Evolution","citation":{"chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784"},"date_published":"2019-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"abstract":[{"text":"In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Preprint","title":"Lower and upper bounds for the waists of different spaces","status":"public","intvolume":" 53","_id":"6634","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","page":"457-490","publication":"Topological Methods in Nonlinear Analysis","citation":{"ama":"Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490. doi:10.12775/TMNA.2019.008","ieee":"A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53, no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019.","apa":"Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008","ista":"Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490.","short":"A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis 53 (2019) 457–490.","mla":"Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008.","chicago":"Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008."},"ec_funded":1,"date_created":"2019-07-14T21:59:19Z","date_updated":"2023-08-29T06:32:48Z","volume":53,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"first_name":"Alfredo","last_name":"Hubard","full_name":"Hubard, Alfredo"},{"full_name":"Karasev, Roman","first_name":"Roman","last_name":"Karasev"}],"publication_status":"published","publisher":"Akademicka Platforma Czasopism","department":[{"_id":"HeEd"}],"year":"2019","month":"06","language":[{"iso":"eng"}],"doi":"10.12775/TMNA.2019.008","isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.06926","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1612.06926"],"isi":["000472541600004"]}},{"ec_funded":1,"year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Elsevier","author":[{"first_name":"André ","last_name":"Silva","full_name":"Silva, André "},{"full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","first_name":"Alan M"},{"first_name":"Bruce","last_name":"Richter","full_name":"Richter, Bruce"},{"full_name":"Lee, Orlando","first_name":"Orlando","last_name":"Lee"}],"date_updated":"2023-08-29T06:31:41Z","date_created":"2019-07-14T21:59:20Z","volume":342,"month":"11","publication_identifier":{"issn":["0012-365X"]},"external_id":{"arxiv":["1901.09955"],"isi":["000486358100025"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.09955","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.disc.2019.06.031","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one."}],"issue":"11","_id":"6638","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Graphs with at most one crossing","status":"public","intvolume":" 342","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Discrete Mathematics","citation":{"ista":"Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one crossing. Discrete Mathematics. 342(11), 3201–3207.","ieee":"A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207, 2019.","apa":"Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031","ama":"Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing. Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031","chicago":"Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031.","mla":"Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics, vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031.","short":"A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342 (2019) 3201–3207."},"page":"3201-3207","date_published":"2019-11-01T00:00:00Z"},{"status":"public","publication_status":"published","title":"Cell division and tissue mechanics","publisher":"Elsevier","department":[{"_id":"CaHe"}],"intvolume":" 60","_id":"6631","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-29T06:33:14Z","date_created":"2019-07-14T21:59:17Z","oa_version":"None","volume":60,"author":[{"id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","last_name":"Godard","full_name":"Godard, Benoit G"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","abstract":[{"text":"The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis.","lang":"eng"}],"quality_controlled":"1","isi":1,"page":"114-120","publication":"Current Opinion in Cell Biology","citation":{"ama":"Godard BG, Heisenberg C-PJ. Cell division and tissue mechanics. Current Opinion in Cell Biology. 2019;60:114-120. doi:10.1016/j.ceb.2019.05.007","ista":"Godard BG, Heisenberg C-PJ. 2019. Cell division and tissue mechanics. Current Opinion in Cell Biology. 60, 114–120.","apa":"Godard, B. G., & Heisenberg, C.-P. J. (2019). Cell division and tissue mechanics. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.05.007","ieee":"B. G. Godard and C.-P. J. Heisenberg, “Cell division and tissue mechanics,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 114–120, 2019.","mla":"Godard, Benoit G., and Carl-Philipp J. Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 114–20, doi:10.1016/j.ceb.2019.05.007.","short":"B.G. Godard, C.-P.J. Heisenberg, Current Opinion in Cell Biology 60 (2019) 114–120.","chicago":"Godard, Benoit G, and Carl-Philipp J Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.05.007."},"external_id":{"isi":["000486545800016"]},"language":[{"iso":"eng"}],"date_published":"2019-10-01T00:00:00Z","doi":"10.1016/j.ceb.2019.05.007","scopus_import":"1","month":"10","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0955-0674"]}},{"language":[{"iso":"eng"}],"doi":"10.1145/3306346.3322992","project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000475740600085"]},"oa":1,"publication_identifier":{"issn":["0730-0301"]},"month":"07","volume":38,"date_updated":"2023-08-29T06:40:49Z","date_created":"2019-07-22T07:22:28Z","author":[{"full_name":"Sumin, Denis","last_name":"Sumin","first_name":"Denis"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"full_name":"Rittig, Tobias","last_name":"Rittig","first_name":"Tobias"},{"full_name":"Babaei, Vahid","first_name":"Vahid","last_name":"Babaei"},{"first_name":"Thomas","last_name":"Nindel","full_name":"Nindel, Thomas"},{"first_name":"Alexander","last_name":"Wilkie","full_name":"Wilkie, Alexander"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"last_name":"Křivánek","first_name":"Jaroslav","full_name":"Křivánek, Jaroslav"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"}],"department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:36Z","article_number":"111","date_published":"2019-07-04T00:00:00Z","citation":{"chicago":"Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992.","mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.","short":"D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).","ista":"Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111.","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992","ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992"},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2019_ACM_Sumin_AuthorVersion.pdf","content_type":"application/pdf","file_size":10109800,"creator":"dernst","relation":"main_file","file_id":"6669","checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","date_created":"2019-07-24T07:36:08Z","date_updated":"2020-07-14T12:47:36Z"},{"file_name":"sumin19geometry-aware-suppl.zip","access_level":"open_access","creator":"dernst","file_size":11051245,"content_type":"application/zip","file_id":"6938","relation":"supplementary_material","date_created":"2019-10-11T06:51:07Z","date_updated":"2020-07-14T12:47:36Z","checksum":"f80f365a04e35855fa467ea7ab26b16c"}],"oa_version":"Submitted Version","intvolume":" 38","status":"public","title":"Geometry-aware scattering compensation for 3D printing","ddc":["000"],"_id":"6660","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","abstract":[{"text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers.","lang":"eng"}],"type":"journal_article"}]