[{"issue":"3","abstract":[{"lang":"eng","text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7245","date_created":"2020-01-09T10:55:58Z","date_updated":"2020-07-14T12:47:13Z","checksum":"ef24572d6ebcc1452c067e05410cc4a2","file_name":"2019_Trends_Evolution_Faria.pdf","access_level":"open_access","file_size":1946795,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","intvolume":" 34","ddc":["570"],"title":"Evolving inversions","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5911","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"239-248","article_type":"original","citation":{"apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005."},"publication":"Trends in Ecology and Evolution","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","volume":34,"date_updated":"2023-08-24T14:29:48Z","date_created":"2019-02-03T22:59:15Z","author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"}],"publisher":"Elsevier","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["01695347"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1016/j.tree.2018.12.005","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000459899000013"]}},{"department":[{"_id":"TaHa"}],"publisher":"European Mathematical Society","publication_status":"published","year":"2019","volume":21,"date_updated":"2023-08-24T14:24:49Z","date_created":"2018-12-11T11:46:29Z","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel","full_name":"Hausel, Tamas"},{"last_name":"Mereb","first_name":"Martin","id":"43D735EE-F248-11E8-B48F-1D18A9856A87","full_name":"Mereb, Martin"},{"last_name":"Wong","first_name":"Michael","full_name":"Wong, Michael"}],"ec_funded":1,"publist_id":"7384","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"language":[{"iso":"eng"}],"doi":"10.4171/JEMS/896","publication_identifier":{"eissn":["1435-9855"]},"month":"10","intvolume":" 21","title":"Arithmetic and representation theory of wild character varieties","status":"public","_id":"439","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system.","lang":"eng"}],"page":"2995-3052","article_type":"original","citation":{"mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.","ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896","ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","apa":"Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896"},"publication":"Journal of the European Mathematical Society","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"_id":"105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","status":"public","intvolume":" 27","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"publication":"European Journal of Human Genetics","citation":{"short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2.","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019.","apa":"Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166."},"article_type":"original","page":"161-166","date_published":"2019-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2019","acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaNo"}],"author":[{"last_name":"Marsh","first_name":"Ashley","full_name":"Marsh, Ashley"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"full_name":"Lockhart, Paul","first_name":"Paul","last_name":"Lockhart"},{"full_name":"Leventer, Richard","first_name":"Richard","last_name":"Leventer"}],"date_updated":"2023-08-24T14:28:24Z","date_created":"2018-12-11T11:44:39Z","volume":27,"publist_id":"7949","oa":1,"external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"main_file_link":[{"url":"https://doi.org/10.1038/s41431-018-0231-2","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41431-018-0231-2","language":[{"iso":"eng"}],"month":"01"},{"publist_id":"7989","author":[{"full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis","first_name":"Konstantinos"},{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gess","first_name":"Benjamin","full_name":"Gess, Benjamin"}],"volume":266,"date_updated":"2023-08-24T14:30:16Z","date_created":"2018-12-11T11:44:26Z","year":"2019","publisher":"Elsevier","department":[{"_id":"JaMa"}],"publication_status":"published","month":"03","doi":"10.1016/j.jde.2018.09.012","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1803.06953"],"isi":["000456332500026"]},"main_file_link":[{"url":"http://arxiv.org/abs/1803.06953","open_access":"1"}],"isi":1,"quality_controlled":"1","issue":"6","abstract":[{"text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"65","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 266","title":"Entropy solutions for stochastic porous media equations","status":"public","article_processing_charge":"No","day":"5","scopus_import":"1","date_published":"2019-03-05T00:00:00Z","citation":{"chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012.","apa":"Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012"},"publication":"Journal of Differential Equations","page":"3732-3763","article_type":"original"},{"citation":{"ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1","ieee":"R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1."},"publication":"Scientific Reports","date_published":"2019-01-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"23","intvolume":" 9","status":"public","title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","ddc":["580"],"_id":"5907","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_ScientificReports_Mocsai.pdf","creator":"dernst","content_type":"application/pdf","file_size":2124292,"file_id":"5923","relation":"main_file","checksum":"4129c7d7663d1f8a1edf8c4232372f66","date_created":"2019-02-05T13:10:02Z","date_updated":"2020-07-14T12:47:13Z"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins."}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000456392400012"]},"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/s41598-018-36884-1","month":"01","publisher":"Nature Publishing Group","department":[{"_id":"FlSc"}],"publication_status":"published","year":"2019","volume":9,"date_created":"2019-02-03T22:59:13Z","date_updated":"2023-08-24T14:33:16Z","author":[{"last_name":"Mócsai","first_name":"Réka","full_name":"Mócsai, Réka"},{"full_name":"Figl, Rudolf","last_name":"Figl","first_name":"Rudolf"},{"full_name":"Troschl, Clemens","first_name":"Clemens","last_name":"Troschl"},{"last_name":"Strasser","first_name":"Richard","full_name":"Strasser, Richard"},{"last_name":"Svehla","first_name":"Elisabeth","full_name":"Svehla, Elisabeth"},{"full_name":"Windwarder, Markus","last_name":"Windwarder","first_name":"Markus"},{"first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas"},{"last_name":"Altmann","first_name":"Friedrich","full_name":"Altmann, Friedrich"}],"article_number":"331","file_date_updated":"2020-07-14T12:47:13Z"},{"month":"01","quality_controlled":"1","isi":1,"external_id":{"isi":["000456336100050"],"pmid":["30610176"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1818099116","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"date_updated":"2023-08-24T14:31:09Z","date_created":"2019-02-03T22:59:14Z","volume":116,"author":[{"full_name":"Lee, Eunkyoung","first_name":"Eunkyoung","last_name":"Lee"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Pérez-Sancho, Jessica","first_name":"Jessica","last_name":"Pérez-Sancho"},{"first_name":"Francisco","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, Francisco"},{"full_name":"Strelau, Matthew","last_name":"Strelau","first_name":"Matthew"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"full_name":"Botella, Miguel A.","first_name":"Miguel A.","last_name":"Botella"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abel","last_name":"Rosado","full_name":"Rosado, Abel"}],"scopus_import":"1","day":"22","article_processing_charge":"No","article_type":"original","page":"1420-1429","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116.","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116.","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","ieee":"E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116"},"date_published":"2019-01-22T00:00:00Z","type":"journal_article","abstract":[{"text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.","lang":"eng"}],"issue":"4","title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","status":"public","intvolume":" 116","_id":"5908","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version"},{"oa_version":"None","intvolume":" 166","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5680","issue":"1","abstract":[{"text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.","lang":"eng"}],"type":"journal_article","date_published":"2019-01-01T00:00:00Z","page":"80-92","citation":{"short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92."},"publication":"Botany Letters","article_processing_charge":"No","day":"01","scopus_import":"1","volume":166,"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-08-24T14:34:12Z","author":[{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"first_name":"Sandrine","last_name":"Paute","full_name":"Paute, Sandrine"},{"full_name":"Lauzeral, Christine","first_name":"Christine","last_name":"Lauzeral"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"publisher":"Taylor and Francis","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","language":[{"iso":"eng"}],"doi":"10.1080/23818107.2018.1545142","isi":1,"quality_controlled":"1","external_id":{"isi":["000463802800009"]},"publication_identifier":{"eissn":["23818115"],"issn":["23818107"]},"month":"01"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"365-394","article_type":"original","citation":{"mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436"},"publication":"Journal of Graph Theory","date_published":"2019-08-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"intvolume":" 91","title":"Extending partial representations of circle graphs","status":"public","_id":"5790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","publication_identifier":{"issn":["03649024"]},"month":"08","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2399"}],"external_id":{"isi":["000485392800004"],"arxiv":["1309.2399"]},"language":[{"iso":"eng"}],"doi":"10.1002/jgt.22436","ec_funded":1,"publisher":"Wiley","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","volume":91,"date_created":"2018-12-30T22:59:15Z","date_updated":"2023-08-24T14:30:43Z","author":[{"first_name":"Steven","last_name":"Chaplick","full_name":"Chaplick, Steven"},{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Klavík, Pavel","last_name":"Klavík","first_name":"Pavel"}]},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.laa.2018.03.002","month":"09","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Elsevier","year":"2019","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","date_updated":"2023-08-24T14:31:47Z","date_created":"2018-12-11T11:46:17Z","volume":576,"author":[{"orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","first_name":"Daniel","full_name":"Virosztek, Daniel"}],"ec_funded":1,"publist_id":"7424","article_type":"original","page":"67-78","publication":"Linear Algebra and Its Applications","citation":{"ama":"Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002."},"date_published":"2019-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Jointly convex quantum Jensen divergences","intvolume":" 576","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"405","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently."}]},{"citation":{"ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","apa":"Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514","chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514.","mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785."},"publication":"Transactions of the American Mathematical Society","page":"5757-5785","date_published":"2019-04-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"175","intvolume":" 371","status":"public","title":"Sieving rational points on varieties","oa_version":"Preprint","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points."}],"main_file_link":[{"url":"https://arxiv.org/abs/1705.01999","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1705.01999"],"isi":["000464034200019"]},"isi":1,"quality_controlled":"1","doi":"10.1090/tran/7514","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00029947"],"eissn":["10886850"]},"month":"04","year":"2019","publisher":"American Mathematical Society","department":[{"_id":"TiBr"}],"publication_status":"published","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"last_name":"Loughran","first_name":"Daniel","full_name":"Loughran, Daniel"}],"volume":371,"date_updated":"2023-08-24T14:34:56Z","date_created":"2018-12-11T11:45:01Z","publist_id":"7746"},{"date_created":"2018-12-11T11:45:48Z","date_updated":"2023-08-24T14:38:32Z","volume":173,"author":[{"last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"JaMa"}],"year":"2019","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","file_date_updated":"2020-07-14T12:46:03Z","publist_id":"7546","language":[{"iso":"eng"}],"doi":"10.1007/s00440-018-0841-1","quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"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":["000463613800001"]},"oa":1,"month":"04","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"file":[{"checksum":"288d16ef7291242f485a9660979486e3","date_created":"2018-12-17T16:25:24Z","date_updated":"2020-07-14T12:46:03Z","relation":"main_file","file_id":"5722","content_type":"application/pdf","file_size":893182,"creator":"dernst","access_level":"open_access","file_name":"2018_ProbTheory_Gerencser.pdf"}],"oa_version":"Published Version","status":"public","title":"Singular SPDEs in domains with boundaries","ddc":["510"],"intvolume":" 173","_id":"319","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition."}],"issue":"3-4","type":"journal_article","date_published":"2019-04-01T00:00:00Z","article_type":"original","page":"697–758","publication":"Probability Theory and Related Fields","citation":{"chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1.","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.","apa":"Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1"},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"month":"02","doi":"10.1007/s00440-018-0835-z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000459396500007"]},"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","ec_funded":1,"publist_id":"7394","file_date_updated":"2020-07-14T12:46:26Z","author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"}],"volume":173,"date_updated":"2023-08-24T14:39:00Z","date_created":"2018-12-11T11:46:25Z","year":"2019","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","publisher":"Springer","department":[{"_id":"LaEr"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","citation":{"ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373.","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z."},"publication":"Probability Theory and Related Fields","page":"293–373","article_type":"original","issue":"1-2","abstract":[{"text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2018_ProbTheory_Ajanki.pdf","access_level":"open_access","file_size":1201840,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5720","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-17T16:12:08Z","checksum":"f9354fa5c71f9edd17132588f0dc7d01"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"429","intvolume":" 173","title":"Stability of the matrix Dyson equation and random matrices with correlations","status":"public","ddc":["510"]},{"month":"01","publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"language":[{"iso":"eng"}],"conference":{"start_date":"2019-01-04","location":"Bangalore, India","end_date":"2019-01-07","name":"ICDCN: Conference on Distributed Computing and Networking"},"doi":"10.1145/3288599.3288617","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000484491600019"],"arxiv":["1809.00896"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00896"}],"date_updated":"2023-08-24T14:41:53Z","date_created":"2019-02-10T22:59:17Z","author":[{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","first_name":"Bapi","last_name":"Chatterjee"},{"last_name":"Peri","first_name":"Sathya","full_name":"Peri, Sathya"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"},{"first_name":"Nandini","last_name":"Singhal","full_name":"Singhal, Nandini"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM","year":"2019","day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-04T00:00:00Z","page":"168-177","publication":"ACM International Conference Proceeding Series","citation":{"ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617","ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.","apa":"Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617."},"abstract":[{"text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.","lang":"eng"}],"type":"conference","oa_version":"Preprint","status":"public","title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","_id":"5947","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Elsevier","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"related_material":{"record":[{"id":"433","status":"public","relation":"earlier_version"}]},"date_created":"2019-01-20T22:59:17Z","date_updated":"2023-08-24T14:39:33Z","volume":259,"external_id":{"isi":["000466061100020"],"arxiv":["1708.08037"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"doi":"10.1016/j.dam.2018.12.025","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0166218X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5857","title":"Thrackles: An improved upper bound","status":"public","intvolume":" 259","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"issue":"4","publication":"Discrete Applied Mathematics","citation":{"short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","apa":"Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231."},"article_type":"original","page":"266-231","date_published":"2019-04-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No"},{"date_published":"2019-01-15T00:00:00Z","publication":"Life","citation":{"ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","short":"B. Corominas-Murtra, Life 9 (2019).","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009."},"day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-11T10:45:27Z","checksum":"7d2322cd96ace41959909b66702d5cf4","file_id":"5951","relation":"main_file","creator":"dernst","file_size":963454,"content_type":"application/pdf","file_name":"2019_Life_Corominas.pdf","access_level":"open_access"}],"oa_version":"Published Version","title":"Thermodynamics of duplication thresholds in synthetic protocell systems","ddc":["570"],"status":"public","intvolume":" 9","_id":"5944","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.","lang":"eng"}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3390/life9010009","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":["000464125500001"]},"month":"01","publication_identifier":{"eissn":["20751729"]},"date_created":"2019-02-10T22:59:15Z","date_updated":"2023-08-24T14:43:41Z","volume":9,"author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat"}],"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"MDPI","year":"2019","file_date_updated":"2020-07-14T12:47:13Z","article_number":"9"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"ama":"Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655","ista":"Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655.","ieee":"M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019.","apa":"Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655","mla":"Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655.","short":"M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).","chicago":"Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655."},"publication":"Frontiers in Chemistry","date_published":"2019-01-24T00:00:00Z","type":"journal_article","abstract":[{"text":"Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.","lang":"eng"}],"intvolume":" 6","ddc":["540"],"title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6029","oa_version":"Published Version","file":[{"file_name":"2019_frontiers_Lindner.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1766820,"file_id":"6039","relation":"main_file","date_created":"2019-02-18T15:10:34Z","date_updated":"2020-07-14T12:47:17Z","checksum":"7841301d7c53b56ef873791b4b6f7b24"}],"publication_identifier":{"eissn":["22962646"]},"month":"01","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000456718000001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fchem.2018.00655","article_number":"655","file_date_updated":"2020-07-14T12:47:17Z","publisher":"Frontiers Media S.A.","department":[{"_id":"JoDa"}],"publication_status":"published","year":"2019","volume":6,"date_created":"2019-02-17T22:59:24Z","date_updated":"2023-08-24T14:45:38Z","author":[{"last_name":"Lindner","first_name":"Marco","full_name":"Lindner, Marco"},{"first_name":"Aliz","last_name":"Tresztenyak","full_name":"Tresztenyak, Aliz"},{"last_name":"Fülöp","first_name":"Gergö","full_name":"Fülöp, Gergö"},{"last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke"},{"first_name":"Adrian","last_name":"Prinz","full_name":"Prinz, Adrian"},{"last_name":"Prinz","first_name":"Iris","full_name":"Prinz, Iris"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"last_name":"Schütz","first_name":"Gerhard J.","full_name":"Schütz, Gerhard J."},{"full_name":"Sevcsik, Eva","last_name":"Sevcsik","first_name":"Eva"}]},{"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000475465000003"]},"quality_controlled":"1","isi":1,"doi":"10.1002/cpa.21816","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:17Z","year":"2019","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Wiley","author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate"},{"last_name":"Hairer","first_name":"Martin","full_name":"Hairer, Martin"}],"date_created":"2019-02-17T22:59:24Z","date_updated":"2023-08-24T14:44:31Z","volume":72,"scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Communications on Pure and Applied Mathematics","citation":{"mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816.","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816"},"page":"1983-2005","date_published":"2019-02-08T00:00:00Z","type":"journal_article","abstract":[{"text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.","lang":"eng"}],"issue":"9","_id":"6028","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["500"],"title":"A solution theory for quasilinear singular SPDEs","intvolume":" 72","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":381350,"file_name":"2019_Wiley_Gerencser.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","date_created":"2020-01-07T13:25:55Z","checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_id":"7237","relation":"main_file"}]},{"external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"isi":1,"quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"conference":{"name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","end_date":"2019-01-15","start_date":"2019-01-13","location":"Cascais, Portugal"},"doi":"10.1007/978-3-030-11245-5_22","language":[{"iso":"eng"}],"month":"01","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"author":[{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"date_updated":"2023-08-24T14:42:22Z","date_created":"2019-02-10T22:59:17Z","volume":11388,"publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","citation":{"short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” International Conference on Verification, Model Checking, and Abstract Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22.","chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In International Conference on Verification, Model Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-11245-5_22.","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: International Conference on Verification, Model Checking, and Abstract Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in International Conference on Verification, Model Checking, and Abstract Interpretation, Cascais, Portugal, 2019, vol. 11388, pp. 468–490.","apa":"Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In International Conference on Verification, Model Checking, and Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-11245-5_22","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490."},"page":"468-490","date_published":"2019-01-11T00:00:00Z","scopus_import":"1","day":"11","article_processing_charge":"No","_id":"5948","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Termination of nondeterministic probabilistic programs","intvolume":" 11388","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs."}]},{"abstract":[{"lang":"eng","text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy."}],"issue":"4","type":"journal_article","oa_version":"Published Version","_id":"5945","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Optimal decoding of cellular identities in a genetic network","intvolume":" 176","day":"07","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-07T00:00:00Z","publication":"Cell","citation":{"ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007","ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.","ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007."},"article_type":"original","page":"844-855.e15","author":[{"full_name":"Petkova, Mariela D.","last_name":"Petkova","first_name":"Mariela D."},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"full_name":"Wieschaus, Eric F.","first_name":"Eric F.","last_name":"Wieschaus"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2019-02-10T22:59:16Z","date_updated":"2023-08-24T14:42:47Z","volume":176,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Cell Press","month":"02","doi":"10.1016/j.cell.2019.01.007","language":[{"iso":"eng"}],"external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.007","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}]},{"volume":863,"date_updated":"2023-08-24T14:43:13Z","date_created":"2019-02-10T22:59:15Z","author":[{"full_name":"Klotz, Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1740-7635","first_name":"Lukasz","last_name":"Klotz"},{"full_name":"Gumowski, Konrad","first_name":"Konrad","last_name":"Gumowski"},{"last_name":"Wesfreid","first_name":"José Eduardo","full_name":"Wesfreid, José Eduardo"}],"department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","publication_status":"published","year":"2019","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2018.974","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1902.07931"],"isi":["000526029100016"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07931"}],"month":"03","oa_version":"Preprint","intvolume":" 863","status":"public","title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5943","abstract":[{"text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.","lang":"eng"}],"type":"journal_article","date_published":"2019-03-25T00:00:00Z","page":"386-406","article_type":"original","citation":{"chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974.","apa":"Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974","ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019.","ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974"},"publication":"Journal of Fluid Mechanics","article_processing_charge":"No","day":"25","scopus_import":"1"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","author":[{"last_name":"Christakis","first_name":"Maria","full_name":"Christakis, Maria"},{"last_name":"Heizmann","first_name":"Matthias","full_name":"Heizmann, Matthias"},{"full_name":"Mansur, Muhammad Numair","first_name":"Muhammad Numair","last_name":"Mansur"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian"},{"last_name":"Wüstholz","first_name":"Valentin","full_name":"Wüstholz, Valentin"}],"volume":11427,"date_updated":"2023-08-24T14:47:45Z","date_created":"2019-02-18T16:44:06Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","month":"04","doi":"10.1007/978-3-030-17462-0_13","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2019-04-11","location":"Prague, Czech Republic","start_date":"2019-04-06"},"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":["000681166500013"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Published Version","file":[{"file_id":"6408","relation":"main_file","checksum":"9998496f6fe202c0a19124b4209154c6","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-05-10T14:16:05Z","access_level":"open_access","file_name":"2019_LNCS_Christakis.pdf","creator":"dernst","file_size":773083,"content_type":"application/pdf"}],"_id":"6042","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11427","ddc":["000"],"title":"Semantic fault localization and suspiciousness ranking","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2019-04-04T00:00:00Z","citation":{"short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13.","chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243."},"publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","page":"226-243"},{"month":"04","publication_identifier":{"isbn":["9781450362825"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control","end_date":"2019-04-18","location":"Montreal, QC, Canada","start_date":"2019-04-16"},"doi":"10.1145/3302504.3311804","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","year":"2019","date_created":"2019-02-18T14:43:28Z","date_updated":"2023-08-24T14:47:21Z","volume":22,"author":[{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"keyword":["reachability analysis","hybrid systems","lazy computation"],"scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"No","page":"39-44","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","citation":{"mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44."},"date_published":"2019-04-16T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems."}],"ddc":["000"],"title":"JuliaReach: A toolbox for set-based reachability","status":"public","intvolume":" 22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6035","file":[{"relation":"main_file","file_id":"6067","date_created":"2019-03-05T09:27:18Z","date_updated":"2020-07-14T12:47:17Z","checksum":"28ed56439aea5991c3122d4730fd828f","file_name":"hscc19.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3784414,"creator":"cschilli"}],"oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41596-018-0117-3","quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000459890700008"],"pmid":["30778205"]},"month":"03","date_updated":"2023-08-24T14:48:33Z","date_created":"2019-02-24T22:59:20Z","volume":14,"author":[{"first_name":"Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"},{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoDa"},{"_id":"Bio"}],"year":"2019","pmid":1,"file_date_updated":"2021-06-29T14:41:46Z","ec_funded":1,"date_published":"2019-03-01T00:00:00Z","article_type":"original","page":"832–863","publication":"Nature Protocols","citation":{"chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3"},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","access_level":"open_access","file_size":84478958,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"kschuh","relation":"main_file","file_id":"9619","date_created":"2021-06-29T14:41:46Z","date_updated":"2021-06-29T14:41:46Z","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","success":1}],"oa_version":"Submitted Version","title":"A practical guide to optimization in X10 expansion microscopy","ddc":["570"],"status":"public","intvolume":" 14","_id":"6052","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.","lang":"eng"}],"issue":"3","type":"journal_article"},{"author":[{"full_name":"Capek, Daniel","last_name":"Capek","first_name":"Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael"},{"full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine","last_name":"Tichy"},{"id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","last_name":"Morri","full_name":"Morri, Maurizio"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"volume":8,"date_updated":"2023-08-24T14:46:01Z","date_created":"2019-02-17T22:59:22Z","year":"2019","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"publisher":"eLife Sciences Publications","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","article_number":"e42093","doi":"10.7554/eLife.42093","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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":["000458025300001"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"02","oa_version":"Published Version","file":[{"checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","date_created":"2019-02-18T15:17:21Z","date_updated":"2020-07-14T12:47:17Z","relation":"main_file","file_id":"6041","content_type":"application/pdf","file_size":5500707,"creator":"dernst","access_level":"open_access","file_name":"2019_elife_Capek.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6025","intvolume":" 8","title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","ddc":["570"],"status":"public","abstract":[{"lang":"eng","text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation."}],"type":"journal_article","date_published":"2019-02-06T00:00:00Z","citation":{"ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093","ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol. 8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093.","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1"},{"month":"02","doi":"10.1371/journal.pbio.2005902","language":[{"iso":"eng"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"external_id":{"isi":["000460317100001"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:17Z","article_number":"e2005902","author":[{"full_name":"Merrill, Richard M.","first_name":"Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","last_name":"Rastas","first_name":"Pasi"},{"full_name":"Martin, Simon H.","last_name":"Martin","first_name":"Simon H."},{"full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado","first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarah","last_name":"Barker","full_name":"Barker, Sarah"},{"full_name":"Davey, John","last_name":"Davey","first_name":"John"},{"full_name":"Mcmillan, W. Owen","last_name":"Mcmillan","first_name":"W. Owen"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9801"}]},"date_created":"2019-02-17T22:59:21Z","date_updated":"2023-08-24T14:46:23Z","volume":17,"year":"2019","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-07T00:00:00Z","publication":"PLoS Biology","citation":{"ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902."},"abstract":[{"text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"access_level":"open_access","file_name":"2019_PLOS_Merrill.pdf","creator":"dernst","file_size":2005949,"content_type":"application/pdf","file_id":"6036","relation":"main_file","checksum":"5f34001617ee729314ca520c049b1112","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-18T14:57:24Z"}],"oa_version":"Published Version","_id":"6022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Genetic dissection of assortative mating behavior","intvolume":" 17"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41477-019-0363-6","isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract"}],"oa":1,"external_id":{"isi":["000460479600014"]},"month":"02","date_created":"2019-02-17T22:59:21Z","date_updated":"2023-08-24T14:46:47Z","volume":5,"author":[{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"last_name":"Van Der Schuren","first_name":"Alja","full_name":"Van Der Schuren, Alja"},{"full_name":"Van Dop, Maritza","last_name":"Van Dop","first_name":"Maritza"},{"full_name":"Van Galen, Luc","last_name":"Van Galen","first_name":"Luc"},{"full_name":"Saiga, Shunsuke","first_name":"Shunsuke","last_name":"Saiga"},{"first_name":"Milad","last_name":"Adibi","full_name":"Adibi, Milad"},{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"last_name":"Ten Hove","first_name":"Colette A.","full_name":"Ten Hove, Colette A."},{"full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter","last_name":"Marhavy"},{"first_name":"Richard","last_name":"Smith","full_name":"Smith, Richard"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"year":"2019","ec_funded":1,"date_published":"2019-02-08T00:00:00Z","page":"160-166","publication":"Nature Plants","citation":{"ieee":"S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6","ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6.","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6."},"day":"08","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","status":"public","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6023","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"issue":"2","type":"journal_article"},{"abstract":[{"text":"Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Quantum electromechanics of a hypersonic crystal","intvolume":" 14","_id":"6053","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-04-01T00:00:00Z","article_type":"original","page":"334–339","publication":"Nature Nanotechnology","citation":{"chicago":"Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2.","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","mla":"Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2.","ieee":"M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.","apa":"Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2","ista":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339.","ama":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2"},"date_updated":"2023-08-24T14:48:08Z","date_created":"2019-02-24T22:59:21Z","volume":14,"author":[{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"full_name":"Mirhosseini, Mohammad","last_name":"Mirhosseini","first_name":"Mohammad"},{"full_name":"Dieterle, Paul B.","last_name":"Dieterle","first_name":"Paul B."},{"full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"year":"2019","month":"04","publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41565-019-0377-2","quality_controlled":"1","isi":1,"external_id":{"isi":["000463195700014"]},"main_file_link":[{"open_access":"1","url":"https://authors.library.caltech.edu/92123/"}],"oa":1},{"month":"01","doi":"10.1090/proc/14240","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1709.02562"],"isi":["000450363900008"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}],"isi":1,"quality_controlled":"1","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Fedorov","first_name":"Roman","full_name":"Fedorov, Roman"}],"volume":147,"date_created":"2019-02-24T22:59:19Z","date_updated":"2023-08-24T14:48:59Z","year":"2019","publisher":"AMS","department":[{"_id":"HeEd"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-01-01T00:00:00Z","citation":{"chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240.","short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240.","apa":"Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240"},"publication":"Proceedings of the American Mathematical Society","page":"91-102","abstract":[{"lang":"eng","text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. "}],"type":"journal_article","oa_version":"Preprint","_id":"6050","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 147","title":"Two circles and only a straightedge","status":"public"},{"day":"07","month":"02","article_processing_charge":"No","citation":{"ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019).","mla":"Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006."},"date_published":"2019-02-07T00:00:00Z","doi":"10.1371/journal.pbio.2005902.s006","type":"research_data_reference","title":"Raw behavioral data","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","year":"2019","_id":"9801","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-24T14:46:23Z","date_created":"2021-08-06T11:34:56Z","oa_version":"Published Version","author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"full_name":"Martin, Simon H.","first_name":"Simon H.","last_name":"Martin"},{"full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","last_name":"Melo Hurtado","first_name":"Maria C"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"full_name":"Davey, John","last_name":"Davey","first_name":"John"},{"last_name":"Mcmillan","first_name":"W. Owen","full_name":"Mcmillan, W. Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6022"}]}},{"date_updated":"2023-08-24T14:50:27Z","date_created":"2019-03-10T22:59:21Z","volume":28,"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"id":"9837","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","file_date_updated":"2020-07-14T12:47:19Z","language":[{"iso":"eng"}],"doi":"10.1111/mec.14972","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":["000465219200013"]},"month":"03","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"file":[{"access_level":"open_access","file_name":"2019_MolecularEcology_Faria.pdf","creator":"dernst","file_size":1510715,"content_type":"application/pdf","file_id":"6097","relation":"main_file","checksum":"f915885756057ec0ca5912a41f46a887","date_created":"2019-03-11T16:12:54Z","date_updated":"2020-07-14T12:47:19Z"}],"oa_version":"Published Version","ddc":["570"],"title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","intvolume":" 28","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6095","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"issue":"6","type":"journal_article","date_published":"2019-03-01T00:00:00Z","page":"1375-1393","publication":"Molecular Ecology","citation":{"mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972","ieee":"R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1088/1751-8121/aaf2dd","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000455379500001"]},"month":"01","volume":52,"date_updated":"2023-08-24T14:49:23Z","date_created":"2019-02-24T22:59:19Z","author":[{"full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"IOP Publishing","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","article_number":"045002","date_published":"2019-01-07T00:00:00Z","citation":{"ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019)."},"publication":"Journal of Physics A: Mathematical and Theoretical","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"07","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"1112304ad363a6d8afaeccece36473cf","date_created":"2019-04-19T12:18:57Z","date_updated":"2020-07-14T12:47:17Z","file_id":"6344","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":1804557,"access_level":"open_access","file_name":"2019_IOP_DeMartino.pdf"}],"intvolume":" 52","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","status":"public","ddc":["570"],"_id":"6049","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","abstract":[{"lang":"eng","text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape."}],"type":"journal_article"},{"ddc":["570"],"status":"public","title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","intvolume":" 8","_id":"6091","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"7b0800d003f14cd06b1802dea0c52941","date_created":"2019-03-11T16:15:37Z","date_updated":"2020-07-14T12:47:19Z","file_id":"6098","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7260753,"access_level":"open_access","file_name":"2019_eLife_Henderson.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"publication":"eLife","citation":{"ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563","ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.","mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563."},"date_published":"2019-02-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"date_created":"2019-03-10T22:59:20Z","date_updated":"2023-08-24T14:50:50Z","volume":8,"author":[{"first_name":"Nathan T.","last_name":"Henderson","full_name":"Henderson, Nathan T."},{"full_name":"Le Marchand, Sylvain J.","first_name":"Sylvain J.","last_name":"Le Marchand"},{"full_name":"Hruska, Martin","last_name":"Hruska","first_name":"Martin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"last_name":"Dalva","first_name":"Matthew B.","full_name":"Dalva, Matthew B."}],"article_number":"e41563","file_date_updated":"2020-07-14T12:47:19Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["30789343"],"isi":["000459380600001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.41563","month":"02"},{"scopus_import":"1","day":"14","article_processing_charge":"No","publication":"Molecular systems biology","citation":{"ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470."},"date_published":"2019-02-14T00:00:00Z","type":"journal_article","abstract":[{"text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.","lang":"eng"}],"issue":"2","status":"public","title":"Temporal order and precision of complex stress responses in individual bacteria","intvolume":" 15","_id":"6046","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","month":"02","isi":1,"quality_controlled":"1","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425","open_access":"1"}],"external_id":{"pmid":["30765425"],"isi":["000459628300003"]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15252/msb.20188470","article_number":"e8470","publication_status":"published","publisher":"Embo Press","department":[{"_id":"GaTk"}],"year":"2019","pmid":1,"date_updated":"2023-08-24T14:49:53Z","date_created":"2019-02-24T22:59:18Z","volume":15,"author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953.","mla":"Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology, vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 88(4), 566–578.","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance,” Journal of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953","ama":"Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953"},"publication":"Journal of Animal Ecology","page":"566-578","article_type":"original","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"6105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 88","ddc":["570"],"title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","status":"public","file":[{"file_id":"6107","relation":"main_file","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T07:43:06Z","checksum":"405cde15120de26018b3bd0dfa29986c","file_name":"2019_JournalAnimalEcology_Kutzer.pdf","access_level":"open_access","creator":"dernst","file_size":1460662,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":" Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.\r\n Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.\r\n We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.\r\n","lang":"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":["000467994800007"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"doi":"10.1111/1365-2656.12953","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["13652656"],"issn":["00218790"]},"month":"04","year":"2019","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","related_material":{"record":[{"id":"9806","status":"public","relation":"research_data"}]},"author":[{"full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","first_name":"Megan"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"full_name":"Armitage, Sophie A.O.","last_name":"Armitage","first_name":"Sophie A.O."}],"volume":88,"date_updated":"2023-08-25T08:04:53Z","date_created":"2019-03-17T22:59:15Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:19Z"},{"volume":16,"date_created":"2019-03-10T22:59:19Z","date_updated":"2023-08-25T08:02:51Z","author":[{"full_name":"Traxl, Alexander","first_name":"Alexander","last_name":"Traxl"},{"full_name":"Mairinger, Severin","first_name":"Severin","last_name":"Mairinger"},{"full_name":"Filip, Thomas","last_name":"Filip","first_name":"Thomas"},{"full_name":"Sauberer, Michael","last_name":"Sauberer","first_name":"Michael"},{"first_name":"Johann","last_name":"Stanek","full_name":"Stanek, Johann"},{"first_name":"Stefan","last_name":"Poschner","full_name":"Poschner, Stefan"},{"full_name":"Jäger, Walter","last_name":"Jäger","first_name":"Walter"},{"full_name":"Zoufal, Viktoria","last_name":"Zoufal","first_name":"Viktoria"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"full_name":"Tournier, Nicolas","first_name":"Nicolas","last_name":"Tournier"},{"full_name":"Bauer, Martin","last_name":"Bauer","first_name":"Martin"},{"full_name":"Wanek, Thomas","first_name":"Thomas","last_name":"Wanek"},{"last_name":"Langer","first_name":"Oliver","full_name":"Langer, Oliver"}],"publisher":"American Chemical Society","department":[{"_id":"GaNo"}],"publication_status":"published","pmid":1,"year":"2019","language":[{"iso":"eng"}],"doi":"10.1021/acs.molpharmaceut.8b01217","isi":1,"quality_controlled":"1","external_id":{"isi":["000460600400031"],"pmid":["30694684"]},"month":"03","oa_version":"None","intvolume":" 16","title":"Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6088","issue":"3","abstract":[{"text":"P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two efflux transporters at the blood–brain barrier (BBB), which effectively restrict brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for a more effective treatment of brain diseases. In the present study, seven marketed drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2 inhibitory properties, were screened for their inhibitory potency at the BBB in vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate [11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v. bolus injections at 30 min before the start of the PET scan, followed by a continuous i.v. infusion for the duration of the PET scan. Five of the tested drugs increased total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, + 25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma concentrations of the tested drugs at the time of the PET scan were higher than clinically achievable plasma concentrations. Some of the tested drugs led to significant increases in blood radioactivity concentrations measured at the end of the PET scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1 and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain delivery despite the administration of high i.v. doses as well as peripheral drug–drug interactions due to transporter inhibition in clearance organs question the translatability of this concept.","lang":"eng"}],"type":"journal_article","date_published":"2019-03-04T00:00:00Z","page":"1282-1293","citation":{"mla":"Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics, vol. 16, no. 3, American Chemical Society, 2019, pp. 1282–93, doi:10.1021/acs.molpharmaceut.8b01217.","short":"A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W. Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular Pharmaceutics 16 (2019) 1282–1293.","chicago":"Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics. American Chemical Society, 2019. https://doi.org/10.1021/acs.molpharmaceut.8b01217.","ama":"Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 2019;16(3):1282-1293. doi:10.1021/acs.molpharmaceut.8b01217","ista":"Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W, Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 16(3), 1282–1293.","ieee":"A. Traxl et al., “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Molecular Pharmaceutics, vol. 16, no. 3. American Chemical Society, pp. 1282–1293, 2019.","apa":"Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S., … Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. American Chemical Society. https://doi.org/10.1021/acs.molpharmaceut.8b01217"},"publication":"Molecular Pharmaceutics","article_processing_charge":"No","day":"04","scopus_import":"1"},{"ec_funded":1,"volume":176,"date_updated":"2023-08-25T08:02:23Z","date_created":"2019-03-10T22:59:19Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Xia, Peng","first_name":"Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","month":"03","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"doi":"10.1016/j.cell.2019.01.019","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["30773315"],"isi":["000460509600013"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.019"}],"oa":1,"issue":"6","abstract":[{"text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 176","title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6087","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2019-03-07T00:00:00Z","page":"1379-1392.e14","article_type":"original","citation":{"ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.","apa":"Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019","ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019.","chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019."},"publication":"Cell"},{"abstract":[{"text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.","lang":"eng"}],"type":"research_data_reference","author":[{"full_name":"Kutzer, Megan","first_name":"Megan","last_name":"Kutzer","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Armitage","first_name":"Sophie A.O.","full_name":"Armitage, Sophie A.O."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6105"}]},"date_created":"2021-08-06T12:06:40Z","date_updated":"2023-08-25T08:04:52Z","oa_version":"Published Version","_id":"9806","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","status":"public","department":[{"_id":"SyCr"}],"publisher":"Dryad","day":"05","month":"02","article_processing_charge":"No","date_published":"2019-02-05T00:00:00Z","doi":"10.5061/dryad.9kj41f0","citation":{"ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","mla":"Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1601.06118","open_access":"1"}],"oa":1,"external_id":{"isi":["000459725600012"],"arxiv":["1601.06118"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1017/etds.2017.52","language":[{"iso":"eng"}],"month":"04","year":"2019","publisher":"Cambridge University Press","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","last_name":"Sadel","first_name":"Christian","full_name":"Sadel, Christian"},{"full_name":"Xu, Disheng","last_name":"Xu","first_name":"Disheng"}],"volume":39,"date_updated":"2023-08-25T08:03:30Z","date_created":"2019-03-10T22:59:18Z","ec_funded":1,"citation":{"ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098.","ieee":"C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019.","apa":"Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2017.52","ama":"Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098. doi:10.1017/etds.2017.52","chicago":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52.","mla":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52.","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098."},"publication":"Ergodic Theory and Dynamical Systems","page":"1082-1098","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"6086","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 39","title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","status":"public","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part."}]},{"publication":"Light: Science and Applications","citation":{"ama":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 2019;8(1). doi:10.1038/s41377-019-0124-3","apa":"Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., & Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. Springer Nature. https://doi.org/10.1038/s41377-019-0124-3","ieee":"B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” Light: Science and Applications, vol. 8, no. 1. Springer Nature, 2019.","ista":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","mla":"Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications, vol. 8, no. 1, 28, Springer Nature, 2019, doi:10.1038/s41377-019-0124-3.","chicago":"Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications. Springer Nature, 2019. https://doi.org/10.1038/s41377-019-0124-3."},"date_published":"2019-03-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6102","status":"public","ddc":["530"],"title":"A full vectorial mapping of nanophotonic light fields","intvolume":" 8","file":[{"file_id":"6108","relation":"main_file","date_created":"2019-03-18T08:08:22Z","date_updated":"2020-07-14T12:47:19Z","checksum":"d71e528cff9c56f70ccc29dd7005257f","file_name":"2019_Light_LeFeber.pdf","access_level":"open_access","creator":"dernst","file_size":1119947,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.","lang":"eng"}],"issue":"1","external_id":{"arxiv":["1803.10145"],"isi":["000460470700004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41377-019-0124-3","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["20477538"],"issn":["20955545"]},"year":"2019","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","author":[{"first_name":"B.","last_name":"Le Feber","full_name":"Le Feber, B."},{"last_name":"Sipe","first_name":"J. E.","full_name":"Sipe, J. E."},{"full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuipers","first_name":"L.","full_name":"Kuipers, L."},{"full_name":"Rotenberg, N.","first_name":"N.","last_name":"Rotenberg"}],"date_created":"2019-03-17T22:59:13Z","date_updated":"2023-08-25T08:06:10Z","volume":8,"article_number":"28","file_date_updated":"2020-07-14T12:47:19Z"},{"month":"02","publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"language":[{"iso":"eng"}],"doi":"10.1093/pcp/pcz001","isi":1,"quality_controlled":"1","external_id":{"pmid":["30668780"],"isi":["000459634300002"]},"date_created":"2019-03-17T22:59:14Z","date_updated":"2023-08-25T08:05:28Z","volume":60,"author":[{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"full_name":"Tamizhselvan, Prashanth","last_name":"Tamizhselvan","first_name":"Prashanth"},{"last_name":"Madhavan","first_name":"Sharmila","full_name":"Madhavan, Sharmila"},{"full_name":"Ryad, Eman Elrefaay","first_name":"Eman Elrefaay","last_name":"Ryad"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre"},{"last_name":"Vanková","first_name":"Radomira","full_name":"Vanková, Radomira"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Tognetti","first_name":"Vanesa B.","full_name":"Tognetti, Vanesa B."}],"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","page":"255-273","publication":"Plant and Cell Physiology","citation":{"ista":"Zwiewka M, Bielach A, Tamizhselvan P, Madhavan S, Ryad EE, Tan S, Hrtyan M, Dobrev P, Vanková R, Friml J, Tognetti VB. 2019. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. 60(2), 255–273.","ieee":"M. Zwiewka et al., “Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking,” Plant and Cell Physiology, vol. 60, no. 2. Oxford University Press, pp. 255–273, 2019.","apa":"Zwiewka, M., Bielach, A., Tamizhselvan, P., Madhavan, S., Ryad, E. E., Tan, S., … Tognetti, V. B. (2019). Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcz001","ama":"Zwiewka M, Bielach A, Tamizhselvan P, et al. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. 2019;60(2):255-273. doi:10.1093/pcp/pcz001","chicago":"Zwiewka, Marta, Agnieszka Bielach, Prashanth Tamizhselvan, Sharmila Madhavan, Eman Elrefaay Ryad, Shutang Tan, Mónika Hrtyan, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” Plant and Cell Physiology. Oxford University Press, 2019. https://doi.org/10.1093/pcp/pcz001.","mla":"Zwiewka, Marta, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” Plant and Cell Physiology, vol. 60, no. 2, Oxford University Press, 2019, pp. 255–73, doi:10.1093/pcp/pcz001.","short":"M. Zwiewka, A. Bielach, P. Tamizhselvan, S. Madhavan, E.E. Ryad, S. Tan, M. Hrtyan, P. Dobrev, R. Vanková, J. Friml, V.B. Tognetti, Plant and Cell Physiology 60 (2019) 255–273."},"abstract":[{"lang":"eng","text":"Abiotic stress poses constant challenges for plant survival and is a serious problem for global agricultural productivity. On a molecular level, stress conditions result in elevation of reactive oxygen species (ROS) production causing oxidative stress associated with oxidation of proteins and nucleic acids as well as impairment of membrane functions. Adaptation of root growth to ROS accumulation is facilitated through modification of auxin and cytokinin hormone homeostasis. Here, we report that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM). Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show that the PIN2 intracellular trafficking during adaptation to oxidative stress requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles. We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent trafficking of PIN2. This mechanism provides a way how root growth acclimates to stress and adapts to a changing environment."}],"issue":"2","type":"journal_article","oa_version":"None","title":"Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking","status":"public","intvolume":" 60","_id":"6104","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1","date_published":"2019-03-19T00:00:00Z","page":"5344-5349","citation":{"chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116.","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"12","abstract":[{"text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3456045,"creator":"dernst","file_name":"2019_PNAS_Recho.pdf","access_level":"open_access","date_created":"2019-04-03T14:10:30Z","date_updated":"2020-07-14T12:47:23Z","checksum":"8b67eee0ea8e5db61583e4d485215258","relation":"main_file","file_id":"6193"}],"intvolume":" 116","title":"Theory of mechanochemical patterning in biphasic biological tissues","status":"public","ddc":["570"],"_id":"6191","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1813255116","project":[{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:23Z","volume":116,"date_created":"2019-03-31T21:59:13Z","date_updated":"2023-08-25T08:57:30Z","related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"author":[{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"full_name":"Hallou, Adrien","last_name":"Hallou","first_name":"Adrien"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2019"},{"author":[{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko","last_name":"Roblek","full_name":"Roblek, Marko"},{"last_name":"Protsyuk","first_name":"Darya","full_name":"Protsyuk, Darya"},{"full_name":"Becker, Paul F.","first_name":"Paul F.","last_name":"Becker"},{"last_name":"Stefanescu","first_name":"Cristina","full_name":"Stefanescu, 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"},{"first_name":"Mathias","last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias"},{"first_name":"Bruno","last_name":"Luckow","full_name":"Luckow, Bruno"},{"first_name":"Stefan W.","last_name":"Schneider","full_name":"Schneider, Stefan W."},{"full_name":"Borsig, Lubor","first_name":"Lubor","last_name":"Borsig"}],"volume":17,"date_created":"2019-03-31T21:59:12Z","date_updated":"2023-08-25T08:57:01Z","pmid":1,"year":"2019","department":[{"_id":"DaSi"}],"publisher":"AACR","publication_status":"published","doi":"10.1158/1541-7786.MCR-18-0530","language":[{"iso":"eng"}],"external_id":{"pmid":["30552233"],"isi":["000460099800012"]},"main_file_link":[{"url":"https://doi.org/10.1158/1541-7786.MCR-18-0530","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["15573125"],"issn":["15417786"]},"month":"03","oa_version":"Published Version","_id":"6190","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 17","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","status":"public","issue":"3","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2019-03-01T00:00:00Z","citation":{"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.","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.","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","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"},"publication":"Molecular Cancer Research","page":"783-793","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"oa_version":"Published Version","file":[{"checksum":"130d7544b57df4a6787e1263c2d7ea43","date_updated":"2020-07-14T12:47:24Z","date_created":"2019-04-11T11:43:38Z","file_id":"6293","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":298466,"access_level":"open_access","file_name":"2019_eLife_Barton.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6230","intvolume":" 8","title":"Why structure matters","status":"public","ddc":["570"],"abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"type":"journal_article","date_published":"2019-03-21T00:00:00Z","citation":{"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.","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","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.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380."},"publication":"eLife","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/"}]},"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"},{"first_name":"Magnus","last_name":"Nordborg","full_name":"Nordborg, Magnus"}],"volume":8,"date_updated":"2023-08-25T08:59:38Z","date_created":"2019-04-07T21:59:15Z","year":"2019","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:24Z","article_number":"e45380","doi":"10.7554/eLife.45380","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":["000461988300001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2050084X"]},"month":"03"},{"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"year":"2019","date_updated":"2023-08-25T08:59:11Z","date_created":"2019-04-07T21:59:15Z","volume":47,"author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"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","month":"03","publication_identifier":{"issn":["00911798"]},"title":"Boundary regularity of stochastic PDEs","status":"public","intvolume":" 47","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6232","oa_version":"Preprint","type":"journal_article","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."}],"issue":"2","page":"804-834","publication":"Annals of Probability","citation":{"chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","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.","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.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272"},"date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"month":"06","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313x"]},"external_id":{"pmid":["30821050"],"isi":["000473644100008"]},"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","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"doi":"10.1111/tpj.14301","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:25Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","last_name":"Valošek","first_name":"Petr","full_name":"Valošek, Petr"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-25T10:11:03Z","date_created":"2019-04-09T08:46:44Z","volume":98,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"The Plant Journal","citation":{"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.","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","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.","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."},"article_type":"original","page":"1048-1059","date_published":"2019-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development."}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6262","ddc":["580"],"title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","status":"public","intvolume":" 98","file":[{"date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-15T09:38:43Z","checksum":"ad3b5e270b67ba2a45f894ce3be27920","file_id":"6304","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1383100,"file_name":"2019_PlantJournal_Rakusov.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"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."}],"type":"journal_article","file":[{"file_name":"2018_MatrixBiology_Davies.pdf","access_level":"open_access","file_size":4444339,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7825","date_updated":"2020-07-14T12:47:27Z","date_created":"2020-05-14T09:02:07Z","checksum":"790878cd78bfc54a147ddcc7c8f286a0"}],"oa_version":"Submitted Version","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","article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2019-05-01T00:00:00Z","page":"47-59","article_type":"original","citation":{"ieee":"H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier, 2019. https://doi.org/10.1016/j.matbio.2018.12.002.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002."},"publication":"Matrix Biology","file_date_updated":"2020-07-14T12:47:27Z","volume":"78-79","date_created":"2019-04-11T20:55:01Z","date_updated":"2023-08-25T10:11:28Z","author":[{"first_name":"Heather S.","last_name":"Davies","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S."},{"full_name":"El Amri, Nouha","first_name":"Nouha","last_name":"El Amri"},{"full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente","first_name":"Liliane"},{"full_name":"Verdier, Claude","last_name":"Verdier","first_name":"Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"last_name":"Richter","first_name":"Ralf P.","full_name":"Richter, Ralf P."},{"full_name":"Débarre, Delphine","last_name":"Débarre","first_name":"Delphine"}],"publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["0945-053X"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.matbio.2018.12.002","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"]}},{"month":"06","publication_identifier":{"issn":["00018708"],"eissn":["10902082"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2019.04.031","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000468857300025"],"arxiv":["1810.08426"]},"file_date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-16T09:13:25Z","date_updated":"2023-08-25T10:11:55Z","volume":349,"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"last_name":"Hu","first_name":"L.Q.","full_name":"Hu, L.Q."}],"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Elsevier","year":"2019","day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-20T00:00:00Z","page":"920-940","publication":"Advances in Mathematics","citation":{"short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.","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.","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.","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","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","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.","ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940."},"abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"file_id":"6311","relation":"main_file","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","date_created":"2019-04-16T09:12:20Z","date_updated":"2020-07-14T12:47:27Z","access_level":"open_access","file_name":"wliqun.pdf","creator":"tbrownin","file_size":379158,"content_type":"application/pdf"}],"oa_version":"Submitted Version","ddc":["512"],"title":"Counting rational points on biquadratic hypersurfaces","status":"public","intvolume":" 349","_id":"6310","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2019-05-01T00:00:00Z","page":"22-25","article_type":"letter_note","citation":{"chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","apa":"Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305","ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp. 22–25, 2019.","ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305"},"publication":"Plant Physiology","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","intvolume":" 180","status":"public","title":"Nitrate modulates the differentiation of root distal stem cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6261","issue":"1","abstract":[{"lang":"eng","text":"Nitrate regulation of root stem cell activity is auxin-dependent."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1104/pp.18.01305","quality_controlled":"1","isi":1,"external_id":{"pmid":["30787134"],"isi":["000466860800010"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.18.01305"}],"oa":1,"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"month":"05","volume":180,"date_created":"2019-04-09T08:46:17Z","date_updated":"2023-08-25T10:10:23Z","author":[{"first_name":"Y","last_name":"Wang","full_name":"Wang, Y"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"}],"department":[{"_id":"JiFr"}],"publisher":"ASPB","publication_status":"published","pmid":1,"year":"2019"},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"12","citation":{"chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z","ieee":"A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z"},"publication":"Molecular Biology Reports","date_published":"2019-04-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure."}],"ddc":["570"],"title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","status":"public","_id":"6352","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2019_MolecularBioReport_Temnov.pdf","access_level":"open_access","creator":"dernst","file_size":1948014,"content_type":"application/pdf","file_id":"6362","relation":"main_file","date_created":"2019-04-30T09:52:36Z","date_updated":"2020-07-14T12:47:28Z","checksum":"45bf040bbce1cea274f6013fa18ba21b"}],"oa_version":"Published Version","publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"month":"04","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":["000470332600049"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11033-019-04765-z","file_date_updated":"2020-07-14T12:47:28Z","department":[{"_id":"LeSa"}],"publisher":"Springer","publication_status":"published","year":"2019","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","date_updated":"2023-08-25T10:14:26Z","date_created":"2019-04-28T21:59:14Z","author":[{"full_name":"Temnov, Andrey Alexandrovich","first_name":"Andrey Alexandrovich","last_name":"Temnov"},{"last_name":"Rogov","first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich"},{"first_name":"Alla Nikolaevna","last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna"},{"first_name":"Elena Valerievna","last_name":"Klychnikova","full_name":"Klychnikova, Elena Valerievna"},{"last_name":"Hartl","first_name":"Markus","full_name":"Hartl, Markus"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"full_name":"Charnagalov, Alexej","first_name":"Alexej","last_name":"Charnagalov","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87"}]},{"_id":"6348","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Resonant electro-optic frequency comb","intvolume":" 568","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"7752","publication":"Nature","citation":{"apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","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","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"author":[{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R"},{"last_name":"Sedlmeir","first_name":"Florian","full_name":"Sedlmeir, Florian"},{"last_name":"Kumari","first_name":"Madhuri","full_name":"Kumari, Madhuri"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"date_created":"2019-04-28T21:59:13Z","date_updated":"2023-08-25T10:15:25Z","volume":568,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.10608"}],"external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41586-019-1110-x","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]}}]