[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 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.","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","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","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.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248."},"title":"Evolving inversions","external_id":{"isi":["000459899000013"]},"article_processing_charge":"No","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"Trends in Ecology and Evolution","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-02-03T22:59:15Z","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.tree.2018.12.005","page":"239-248","oa":1,"quality_controlled":"1","publisher":"Elsevier","ddc":["570"],"date_updated":"2023-08-24T14:29:48Z","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"NiBa"}],"_id":"5911","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_size":1946795,"date_updated":"2020-07-14T12:47:13Z","creator":"cziletti","file_name":"2019_Trends_Evolution_Faria.pdf","date_created":"2020-01-09T10:55:58Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ef24572d6ebcc1452c067e05410cc4a2","file_id":"7245"}],"publication_status":"published","publication_identifier":{"issn":["01695347"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"issue":"3","volume":34,"oa_version":"Published Version","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."}],"intvolume":" 34","month":"03","scopus_import":"1"},{"status":"public","article_type":"original","type":"journal_article","_id":"439","department":[{"_id":"TaHa"}],"date_updated":"2023-08-24T14:24:49Z","month":"10","intvolume":" 21","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"oa_version":"Preprint","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"}],"volume":21,"issue":"10","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1435-9855"]},"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593"}],"title":"Arithmetic and representation theory of wild character varieties","publist_id":"7384","author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Hausel, Tamas"},{"first_name":"Martin","id":"43D735EE-F248-11E8-B48F-1D18A9856A87","full_name":"Mereb, Martin","last_name":"Mereb"},{"first_name":"Michael","last_name":"Wong","full_name":"Wong, Michael"}],"article_processing_charge":"No","external_id":{"arxiv":["1604.03382"],"isi":["000480413600002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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","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.","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.","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."},"quality_controlled":"1","publisher":"European Mathematical Society","oa":1,"date_published":"2019-10-01T00:00:00Z","doi":"10.4171/JEMS/896","date_created":"2018-12-11T11:46:29Z","page":"2995-3052","day":"01","publication":"Journal of the European Mathematical Society","isi":1,"year":"2019"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"161-166","doi":"10.1038/s41431-018-0231-2","date_published":"2019-01-01T00:00:00Z","date_created":"2018-12-11T11:44:39Z","isi":1,"year":"2019","day":"01","publication":"European Journal of Human Genetics","publist_id":"7949","author":[{"first_name":"Ashley","last_name":"Marsh","full_name":"Marsh, Ashley"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"},{"full_name":"Lockhart, Paul","last_name":"Lockhart","first_name":"Paul"},{"last_name":"Leventer","full_name":"Leventer, Richard","first_name":"Richard"}],"article_processing_charge":"No","external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","citation":{"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.","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.","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.","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.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"month":"01","intvolume":" 27","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."}],"pmid":1,"oa_version":"Published Version","volume":27,"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"105","department":[{"_id":"GaNo"}],"date_updated":"2023-08-24T14:28:24Z"},{"department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:30:16Z","type":"journal_article","article_type":"original","status":"public","_id":"65","volume":266,"issue":"6","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"scopus_import":"1","intvolume":" 266","month":"03","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","external_id":{"isi":["000456332500026"],"arxiv":["1803.06953"]},"article_processing_charge":"No","author":[{"last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos","first_name":"Konstantinos"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"first_name":"Benjamin","last_name":"Gess","full_name":"Gess, Benjamin"}],"publist_id":"7989","title":"Entropy solutions for stochastic porous media equations","citation":{"short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","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.","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","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","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.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"3732-3763","date_created":"2018-12-11T11:44:26Z","date_published":"2019-03-05T00:00:00Z","doi":"10.1016/j.jde.2018.09.012","year":"2019","isi":1,"publication":"Journal of Differential Equations","day":"5","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"_id":"5907","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-08-24T14:33:16Z","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"FlSc"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 9","scopus_import":"1","file":[{"checksum":"4129c7d7663d1f8a1edf8c4232372f66","file_id":"5923","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-05T13:10:02Z","file_name":"2019_ScientificReports_Mocsai.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_size":2124292}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9,"issue":"1","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"331","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (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."},"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","author":[{"first_name":"Réka","last_name":"Mócsai","full_name":"Mócsai, Réka"},{"first_name":"Rudolf","last_name":"Figl","full_name":"Figl, Rudolf"},{"first_name":"Clemens","last_name":"Troschl","full_name":"Troschl, Clemens"},{"first_name":"Richard","last_name":"Strasser","full_name":"Strasser, Richard"},{"first_name":"Elisabeth","last_name":"Svehla","full_name":"Svehla, Elisabeth"},{"full_name":"Windwarder, Markus","last_name":"Windwarder","first_name":"Markus"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Thader","full_name":"Thader, Andreas"},{"full_name":"Altmann, Friedrich","last_name":"Altmann","first_name":"Friedrich"}],"article_processing_charge":"No","external_id":{"isi":["000456392400012"]},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"23","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1038/s41598-018-36884-1","date_published":"2019-01-23T00:00:00Z","date_created":"2019-02-03T22:59:13Z"},{"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.","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.","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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000456336100050"],"pmid":["30610176"]},"article_processing_charge":"No","author":[{"full_name":"Lee, Eunkyoung","last_name":"Lee","first_name":"Eunkyoung"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, Jessica","first_name":"Jessica"},{"first_name":"Francisco","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, Francisco"},{"last_name":"Strelau","full_name":"Strelau, Matthew","first_name":"Matthew"},{"last_name":"Macho","full_name":"Macho, Alberto P.","first_name":"Alberto P."},{"full_name":"Botella, Miguel A.","last_name":"Botella","first_name":"Miguel A."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Rosado, Abel","last_name":"Rosado","first_name":"Abel"}],"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","year":"2019","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"22","page":"1420-1429","date_created":"2019-02-03T22:59:14Z","doi":"10.1073/pnas.1818099116","date_published":"2019-01-22T00:00:00Z","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","date_updated":"2023-08-24T14:31:09Z","department":[{"_id":"JiFr"}],"_id":"5908","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":116,"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"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"scopus_import":"1","intvolume":" 116","month":"01"},{"department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:34:12Z","status":"public","type":"journal_article","_id":"5680","volume":166,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23818115"],"issn":["23818107"]},"publication_status":"published","month":"01","intvolume":" 166","scopus_import":"1","oa_version":"None","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"}],"title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","author":[{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"first_name":"Sandrine","last_name":"Paute","full_name":"Paute, Sandrine"},{"last_name":"Lauzeral","full_name":"Lauzeral, Christine","first_name":"Christine"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"}],"article_processing_charge":"No","external_id":{"isi":["000463802800009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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."},"doi":"10.1080/23818107.2018.1545142","date_published":"2019-01-01T00:00:00Z","date_created":"2018-12-16T22:59:20Z","page":"80-92","day":"01","publication":"Botany Letters","isi":1,"year":"2019","quality_controlled":"1","publisher":"Taylor and Francis"},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2399"}],"scopus_import":"1","intvolume":" 91","month":"08","publication_status":"published","publication_identifier":{"issn":["03649024"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"4","volume":91,"_id":"5790","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:30:43Z","department":[{"_id":"UlWa"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2019","isi":1,"publication":"Journal of Graph Theory","day":"01","page":"365-394","date_created":"2018-12-30T22:59:15Z","doi":"10.1002/jgt.22436","date_published":"2019-08-01T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"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.","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","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","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.","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.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1309.2399"],"isi":["000485392800004"]},"article_processing_charge":"No","author":[{"first_name":"Steven","last_name":"Chaplick","full_name":"Chaplick, Steven"},{"last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Klavík, Pavel","last_name":"Klavík","first_name":"Pavel"}],"title":"Extending partial representations of circle graphs"},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":576,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 576","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"scopus_import":"1","date_updated":"2023-08-24T14:31:47Z","department":[{"_id":"LaEr"}],"_id":"405","status":"public","type":"journal_article","article_type":"original","publication":"Linear Algebra and Its Applications","day":"01","year":"2019","isi":1,"date_created":"2018-12-11T11:46:17Z","doi":"10.1016/j.laa.2018.03.002","date_published":"2019-09-01T00:00:00Z","page":"67-78","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)","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","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","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","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.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","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."},"title":"Jointly convex quantum Jensen divergences","article_processing_charge":"No","external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"publist_id":"7424","author":[{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"date_updated":"2023-08-24T14:34:56Z","department":[{"_id":"TiBr"}],"_id":"175","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"publication_status":"published","issue":"8","volume":371,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"04","intvolume":" 371","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.01999","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","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.","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","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.","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785."},"title":"Sieving rational points on varieties","publist_id":"7746","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"first_name":"Daniel","full_name":"Loughran, Daniel","last_name":"Loughran"}],"article_processing_charge":"No","external_id":{"arxiv":["1705.01999"],"isi":["000464034200019"]},"day":"15","publication":"Transactions of the American Mathematical Society","isi":1,"year":"2019","doi":"10.1090/tran/7514","date_published":"2019-04-15T00:00:00Z","date_created":"2018-12-11T11:45:01Z","page":"5757-5785","publisher":"American Mathematical Society","quality_controlled":"1","oa":1},{"month":"04","intvolume":" 173","scopus_import":"1","oa_version":"Published Version","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."}],"volume":173,"issue":"3-4","file":[{"creator":"dernst","file_size":893182,"date_updated":"2020-07-14T12:46:03Z","file_name":"2018_ProbTheory_Gerencser.pdf","date_created":"2018-12-17T16:25:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"288d16ef7291242f485a9660979486e3","file_id":"5722"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"319","file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"JaMa"}],"ddc":["510"],"date_updated":"2023-08-24T14:38:32Z","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","doi":"10.1007/s00440-018-0841-1","date_published":"2019-04-01T00:00:00Z","date_created":"2018-12-11T11:45:48Z","page":"697–758","day":"01","publication":"Probability Theory and Related Fields","has_accepted_license":"1","isi":1,"year":"2019","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"title":"Singular SPDEs in domains with boundaries","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"first_name":"Martin","last_name":"Hairer","full_name":"Hairer, Martin"}],"publist_id":"7546","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000463613800001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","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","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","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.","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758."}},{"day":"01","publication":"Probability Theory and Related Fields","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1007/s00440-018-0835-z","date_published":"2019-02-01T00:00:00Z","date_created":"2018-12-11T11:46:25Z","page":"293–373","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","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."},"title":"Stability of the matrix Dyson equation and random matrices with correlations","publist_id":"7394","author":[{"full_name":"Ajanki, Oskari H","last_name":"Ajanki","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"}],"external_id":{"isi":["000459396500007"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file":[{"date_updated":"2020-07-14T12:46:26Z","file_size":1201840,"creator":"dernst","date_created":"2018-12-17T16:12:08Z","file_name":"2018_ProbTheory_Ajanki.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f9354fa5c71f9edd17132588f0dc7d01","file_id":"5720"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"publication_status":"published","issue":"1-2","volume":173,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"02","intvolume":" 173","scopus_import":"1","ddc":["510"],"date_updated":"2023-08-24T14:39:00Z","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"LaEr"}],"_id":"429","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"publisher":"ACM","quality_controlled":"1","oa":1,"day":"04","publication":"ACM International Conference Proceeding Series","isi":1,"year":"2019","date_published":"2019-01-04T00:00:00Z","doi":"10.1145/3288599.3288617","date_created":"2019-02-10T22:59:17Z","page":"168-177","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177."},"title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","author":[{"first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee"},{"full_name":"Peri, Sathya","last_name":"Peri","first_name":"Sathya"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"},{"first_name":"Nandini","full_name":"Singhal, Nandini","last_name":"Singhal"}],"article_processing_charge":"No","external_id":{"isi":["000484491600019"],"arxiv":["1809.00896"]},"oa_version":"Preprint","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"}],"month":"01","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.00896","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"publication_status":"published","_id":"5947","status":"public","type":"conference","conference":{"start_date":"2019-01-04","end_date":"2019-01-07","location":"Bangalore, India","name":"ICDCN: Conference on Distributed Computing and Networking"},"date_updated":"2023-08-24T14:41:53Z","department":[{"_id":"DaAl"}]},{"type":"journal_article","article_type":"original","status":"public","_id":"5857","department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:39:33Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"scopus_import":"1","intvolume":" 259","month":"04","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","related_material":{"record":[{"id":"433","status":"public","relation":"earlier_version"}]},"issue":"4","volume":259,"publication_status":"published","publication_identifier":{"issn":["0166218X"]},"language":[{"iso":"eng"}],"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"external_id":{"arxiv":["1708.08037"],"isi":["000466061100020"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"title":"Thrackles: An improved upper bound","citation":{"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.","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 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.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"266-231","date_created":"2019-01-20T22:59:17Z","doi":"10.1016/j.dam.2018.12.025","date_published":"2019-04-30T00:00:00Z","year":"2019","isi":1,"publication":"Discrete Applied Mathematics","day":"30"},{"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-08-24T14:43:41Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"5944","volume":9,"issue":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2019_Life_Corominas.pdf","date_created":"2019-02-11T10:45:27Z","file_size":963454,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_id":"5951","checksum":"7d2322cd96ace41959909b66702d5cf4","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["20751729"]},"intvolume":" 9","month":"01","scopus_import":"1","oa_version":"Published Version","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"}],"title":"Thermodynamics of duplication thresholds in synthetic protocell systems","article_processing_charge":"No","external_id":{"isi":["000464125500001"]},"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","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.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9."},"article_number":"9","date_created":"2019-02-10T22:59:15Z","date_published":"2019-01-15T00:00:00Z","doi":"10.3390/life9010009","publication":"Life","day":"15","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"month":"01","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","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"}],"volume":6,"file":[{"checksum":"7841301d7c53b56ef873791b4b6f7b24","file_id":"6039","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_frontiers_Lindner.pdf","date_created":"2019-02-18T15:10:34Z","creator":"dernst","file_size":1766820,"date_updated":"2020-07-14T12:47:17Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22962646"]},"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6029","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JoDa"}],"ddc":["540"],"date_updated":"2023-08-24T14:45:38Z","publisher":"Frontiers Media S.A.","quality_controlled":"1","oa":1,"doi":"10.3389/fchem.2018.00655","date_published":"2019-01-24T00:00:00Z","date_created":"2019-02-17T22:59:24Z","day":"24","publication":"Frontiers in Chemistry","isi":1,"has_accepted_license":"1","year":"2019","article_number":"655","title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","author":[{"first_name":"Marco","last_name":"Lindner","full_name":"Lindner, Marco"},{"last_name":"Tresztenyak","full_name":"Tresztenyak, Aliz","first_name":"Aliz"},{"first_name":"Gergö","full_name":"Fülöp, Gergö","last_name":"Fülöp"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"last_name":"Prinz","full_name":"Prinz, Adrian","first_name":"Adrian"},{"full_name":"Prinz, Iris","last_name":"Prinz","first_name":"Iris"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schütz, Gerhard J.","last_name":"Schütz","first_name":"Gerhard J."},{"full_name":"Sevcsik, Eva","last_name":"Sevcsik","first_name":"Eva"}],"article_processing_charge":"No","external_id":{"isi":["000456718000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","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","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.","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."}},{"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Communications on Pure and Applied Mathematics","day":"08","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-02-17T22:59:24Z","doi":"10.1002/cpa.21816","date_published":"2019-02-08T00:00:00Z","page":"1983-2005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","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.","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.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","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","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"},"title":"A solution theory for quasilinear singular SPDEs","external_id":{"isi":["000475465000003"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"oa_version":"Published Version","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"}],"intvolume":" 72","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_id":"7237","file_size":381350,"date_updated":"2020-07-14T12:47:17Z","creator":"kschuh","file_name":"2019_Wiley_Gerencser.pdf","date_created":"2020-01-07T13:25:55Z"}],"publication_status":"published","volume":72,"issue":"9","_id":"6028","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["500"],"date_updated":"2023-08-24T14:44:31Z","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JaMa"}]},{"quality_controlled":"1","publisher":"Springer Nature","page":"468-490","date_created":"2019-02-10T22:59:17Z","doi":"10.1007/978-3-030-11245-5_22","date_published":"2019-01-11T00:00:00Z","year":"2019","isi":1,"publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","day":"11","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"article_processing_charge":"No","external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"author":[{"first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"title":"Termination of nondeterministic probabilistic programs","citation":{"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.","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.","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.","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 11388","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","volume":11388,"publication_status":"published","language":[{"iso":"eng"}],"conference":{"name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","location":"Cascais, Portugal","end_date":"2019-01-15","start_date":"2019-01-13"},"type":"conference","status":"public","_id":"5948","department":[{"_id":"KrCh"}],"date_updated":"2023-08-24T14:42:22Z"},{"quality_controlled":"1","publisher":"Cell Press","oa":1,"doi":"10.1016/j.cell.2019.01.007","date_published":"2019-02-07T00:00:00Z","date_created":"2019-02-10T22:59:16Z","page":"844-855.e15","day":"07","publication":"Cell","isi":1,"year":"2019","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"title":"Optimal decoding of cellular identities in a genetic network","author":[{"first_name":"Mariela D.","last_name":"Petkova","full_name":"Petkova, Mariela D."},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"full_name":"Wieschaus, Eric F.","last_name":"Wieschaus","first_name":"Eric F."},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"article_processing_charge":"No","external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","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","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","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.","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.","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."},"month":"02","intvolume":" 176","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.007"}],"pmid":1,"oa_version":"Published Version","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."}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/"}]},"volume":176,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"5945","department":[{"_id":"GaTk"}],"date_updated":"2023-08-24T14:42:47Z"},{"day":"25","publication":"Journal of Fluid Mechanics","isi":1,"year":"2019","doi":"10.1017/jfm.2018.974","date_published":"2019-03-25T00:00:00Z","date_created":"2019-02-10T22:59:15Z","page":"386-406","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","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.","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","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","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.","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.","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."},"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","author":[{"last_name":"Klotz","orcid":"0000-0003-1740-7635","full_name":"Klotz, Lukasz","first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gumowski","full_name":"Gumowski, Konrad","first_name":"Konrad"},{"first_name":"José Eduardo","last_name":"Wesfreid","full_name":"Wesfreid, José Eduardo"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.07931"],"isi":["000526029100016"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":863,"ec_funded":1,"oa_version":"Preprint","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"}],"month":"03","intvolume":" 863","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}],"date_updated":"2023-08-24T14:43:13Z","department":[{"_id":"BjHo"}],"_id":"5943","status":"public","article_type":"original","type":"journal_article"},{"status":"public","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Prague, Czech Republic","end_date":"2019-04-11","start_date":"2019-04-06"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"6042","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-24T14:47:45Z","intvolume":" 11427","month":"04","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","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."}],"ec_funded":1,"volume":11427,"language":[{"iso":"eng"}],"file":[{"file_id":"6408","checksum":"9998496f6fe202c0a19124b4209154c6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_LNCS_Christakis.pdf","date_created":"2019-05-10T14:16:05Z","file_size":773083,"date_updated":"2020-07-14T12:47:17Z","creator":"dernst"}],"publication_status":"published","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Semantic fault localization and suspiciousness ranking","external_id":{"isi":["000681166500013"]},"article_processing_charge":"No","author":[{"full_name":"Christakis, Maria","last_name":"Christakis","first_name":"Maria"},{"first_name":"Matthias","full_name":"Heizmann, Matthias","last_name":"Heizmann"},{"first_name":"Muhammad Numair","last_name":"Mansur","full_name":"Mansur, Muhammad Numair"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"},{"full_name":"Wüstholz, Valentin","last_name":"Wüstholz","first_name":"Valentin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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.","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.","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."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2019-02-18T16:44:06Z","doi":"10.1007/978-3-030-17462-0_13","date_published":"2019-04-04T00:00:00Z","page":"226-243","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","day":"04","year":"2019","has_accepted_license":"1","isi":1},{"oa":1,"quality_controlled":"1","publisher":"ACM","year":"2019","isi":1,"has_accepted_license":"1","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","day":"16","page":"39-44","date_created":"2019-02-18T14:43:28Z","date_published":"2019-04-16T00:00:00Z","doi":"10.1145/3302504.3311804","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn","last_name":"Potomkin"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"title":"JuliaReach: A toolbox for set-based reachability","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 22","month":"04","publication_status":"published","publication_identifier":{"isbn":["9781450362825"]},"language":[{"iso":"eng"}],"file":[{"file_id":"6067","checksum":"28ed56439aea5991c3122d4730fd828f","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-03-05T09:27:18Z","file_name":"hscc19.pdf","date_updated":"2020-07-14T12:47:17Z","file_size":3784414,"creator":"cschilli"}],"ec_funded":1,"volume":22,"_id":"6035","conference":{"start_date":"2019-04-16","location":"Montreal, QC, Canada","end_date":"2019-04-18","name":"HSCC: Hybrid Systems Computation and Control"},"type":"conference","keyword":["reachability analysis","hybrid systems","lazy computation"],"status":"public","date_updated":"2023-08-24T14:47:21Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:17Z"},{"_id":"6052","status":"public","type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-24T14:48:33Z","department":[{"_id":"JoDa"},{"_id":"Bio"}],"file_date_updated":"2021-06-29T14:41:46Z","pmid":1,"oa_version":"Submitted Version","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"}],"month":"03","intvolume":" 14","scopus_import":"1","file":[{"file_id":"9619","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","success":1,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"open_access","relation":"main_file","date_created":"2021-06-29T14:41:46Z","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","date_updated":"2021-06-29T14:41:46Z","file_size":84478958,"creator":"kschuh"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":14,"issue":"3","ec_funded":1,"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 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","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","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.","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.","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."},"title":"A practical guide to optimization in X10 expansion microscopy","author":[{"last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"article_processing_charge":"No","external_id":{"isi":["000459890700008"],"pmid":["30778205"]},"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Protocols","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-03-01T00:00:00Z","doi":"10.1038/s41596-018-0117-3","date_created":"2019-02-24T22:59:20Z","page":"832–863"},{"ec_funded":1,"volume":8,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","file_id":"6041","date_updated":"2020-07-14T12:47:17Z","file_size":5500707,"creator":"dernst","date_created":"2019-02-18T15:17:21Z","file_name":"2019_elife_Capek.pdf"}],"scopus_import":"1","intvolume":" 8","month":"02","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:47:17Z","date_updated":"2023-08-24T14:46:01Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"6025","date_created":"2019-02-17T22:59:22Z","doi":"10.7554/eLife.42093","date_published":"2019-02-06T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"eLife","day":"06","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000458025300001"]},"author":[{"first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","last_name":"Capek"},{"last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tichy","full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine"},{"full_name":"Morri, Maurizio","last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","citation":{"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.","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.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"article_number":"e42093"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","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.","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."},"title":"Genetic dissection of assortative mating behavior","author":[{"first_name":"Richard M.","last_name":"Merrill","full_name":"Merrill, Richard M."},{"first_name":"Pasi","full_name":"Rastas, Pasi","last_name":"Rastas"},{"first_name":"Simon H.","full_name":"Martin, Simon H.","last_name":"Martin"},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C"},{"last_name":"Barker","full_name":"Barker, Sarah","first_name":"Sarah"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"last_name":"Mcmillan","full_name":"Mcmillan, W. Owen","first_name":"W. Owen"},{"first_name":"Chris D.","full_name":"Jiggins, Chris D.","last_name":"Jiggins"}],"external_id":{"isi":["000460317100001"]},"article_processing_charge":"No","article_number":"e2005902","day":"07","publication":"PLoS Biology","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-02-07T00:00:00Z","doi":"10.1371/journal.pbio.2005902","date_created":"2019-02-17T22:59:21Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"ddc":["570"],"date_updated":"2023-08-24T14:46:23Z","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"NiBa"}],"_id":"6022","status":"public","type":"journal_article","tmp":{"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)","short":"CC0 (1.0)"},"file":[{"file_name":"2019_PLOS_Merrill.pdf","date_created":"2019-02-18T14:57:24Z","creator":"dernst","file_size":2005949,"date_updated":"2020-07-14T12:47:17Z","checksum":"5f34001617ee729314ca520c049b1112","file_id":"6036","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":17,"related_material":{"record":[{"status":"public","id":"9801","relation":"research_data"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"02","intvolume":" 17","scopus_import":"1"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","external_id":{"isi":["000460479600014"]},"article_processing_charge":"No","author":[{"first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"full_name":"Van Der Schuren, Alja","last_name":"Van Der Schuren","first_name":"Alja"},{"first_name":"Maritza","last_name":"Van Dop","full_name":"Van Dop, Maritza"},{"first_name":"Luc","last_name":"Van Galen","full_name":"Van Galen, Luc"},{"first_name":"Shunsuke","full_name":"Saiga, Shunsuke","last_name":"Saiga"},{"full_name":"Adibi, Milad","last_name":"Adibi","first_name":"Milad"},{"first_name":"Barbara","last_name":"Möller","full_name":"Möller, Barbara"},{"first_name":"Colette A.","full_name":"Ten Hove, Colette A.","last_name":"Ten Hove"},{"last_name":"Marhavy","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Richard","full_name":"Smith, Richard","last_name":"Smith"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-02-17T22:59:21Z","doi":"10.1038/s41477-019-0363-6","date_published":"2019-02-08T00:00:00Z","page":"160-166","publication":"Nature Plants","day":"08","year":"2019","isi":1,"status":"public","type":"journal_article","_id":"6023","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2023-08-24T14:46:47Z","intvolume":" 5","month":"02","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract"}],"scopus_import":"1","oa_version":"Submitted Version","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"}],"ec_funded":1,"volume":5,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"publication_status":"published","issue":"4","volume":14,"oa_version":"Submitted Version","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"}],"month":"04","intvolume":" 14","scopus_import":"1","main_file_link":[{"url":"https://authors.library.caltech.edu/92123/","open_access":"1"}],"date_updated":"2023-08-24T14:48:08Z","department":[{"_id":"JoFi"}],"_id":"6053","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Nature Nanotechnology","isi":1,"year":"2019","date_published":"2019-04-01T00:00:00Z","doi":"10.1038/s41565-019-0377-2","date_created":"2019-02-24T22:59:21Z","page":"334–339","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","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.","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.","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.","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."},"title":"Quantum electromechanics of a hypersonic crystal","author":[{"full_name":"Kalaee, Mahmoud","last_name":"Kalaee","first_name":"Mahmoud"},{"first_name":"Mohammad","full_name":"Mirhosseini, Mohammad","last_name":"Mirhosseini"},{"last_name":"Dieterle","full_name":"Dieterle, Paul B.","first_name":"Paul B."},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"}],"article_processing_charge":"No","external_id":{"isi":["000463195700014"]}},{"volume":147,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 147","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}],"oa_version":"Preprint","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. "}],"department":[{"_id":"HeEd"}],"date_updated":"2023-08-24T14:48:59Z","status":"public","type":"journal_article","_id":"6050","doi":"10.1090/proc/14240","date_published":"2019-01-01T00:00:00Z","date_created":"2019-02-24T22:59:19Z","page":"91-102","day":"01","publication":"Proceedings of the American Mathematical Society","isi":1,"year":"2019","publisher":"AMS","quality_controlled":"1","oa":1,"title":"Two circles and only a straightedge","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Fedorov","full_name":"Fedorov, Roman","first_name":"Roman"}],"external_id":{"arxiv":["1709.02562"],"isi":["000450363900008"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 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","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","short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","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."}},{"type":"research_data_reference","status":"public","_id":"9801","article_processing_charge":"No","author":[{"first_name":"Richard M.","full_name":"Merrill, Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","last_name":"Rastas","first_name":"Pasi"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado"},{"first_name":"Sarah","last_name":"Barker","full_name":"Barker, Sarah"},{"full_name":"Davey, John","last_name":"Davey","first_name":"John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"department":[{"_id":"NiBa"}],"title":"Raw behavioral data","citation":{"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","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006","ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","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.","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.","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."},"date_updated":"2023-08-24T14:46:23Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","month":"02","oa_version":"Published Version","date_created":"2021-08-06T11:34:56Z","related_material":{"record":[{"id":"6022","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2005902.s006","date_published":"2019-02-07T00:00:00Z","year":"2019","day":"07"},{"date_updated":"2023-08-24T14:50:27Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"NiBa"}],"_id":"6095","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publication_status":"published","file":[{"file_name":"2019_MolecularEcology_Faria.pdf","date_created":"2019-03-11T16:12:54Z","file_size":1510715,"date_updated":"2020-07-14T12:47:19Z","creator":"dernst","checksum":"f915885756057ec0ca5912a41f46a887","file_id":"6097","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"9837","relation":"research_data"}]},"issue":"6","volume":28,"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."}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 28","citation":{"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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"external_id":{"isi":["000465219200013"]},"article_processing_charge":"No","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Molecular Ecology","page":"1375-1393","date_published":"2019-03-01T00:00:00Z","doi":"10.1111/mec.14972","date_created":"2019-03-10T22:59:21Z","publisher":"Wiley","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","publisher":"IOP Publishing","date_created":"2019-02-24T22:59:19Z","doi":"10.1088/1751-8121/aaf2dd","date_published":"2019-01-07T00:00:00Z","publication":"Journal of Physics A: Mathematical and Theoretical","day":"07","year":"2019","has_accepted_license":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"045002","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000455379500001"]},"author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","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.","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.","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."},"intvolume":" 52","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"volume":52,"issue":"4","language":[{"iso":"eng"}],"file":[{"file_name":"2019_IOP_DeMartino.pdf","date_created":"2019-04-19T12:18:57Z","file_size":1804557,"date_updated":"2020-07-14T12:47:17Z","creator":"kschuh","checksum":"1112304ad363a6d8afaeccece36473cf","file_id":"6344","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6049","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2023-08-24T14:49:23Z"},{"date_published":"2019-02-21T00:00:00Z","doi":"10.7554/eLife.41563","date_created":"2019-03-10T22:59:20Z","has_accepted_license":"1","isi":1,"year":"2019","day":"21","publication":"eLife","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"author":[{"last_name":"Henderson","full_name":"Henderson, Nathan T.","first_name":"Nathan T."},{"last_name":"Le Marchand","full_name":"Le Marchand, Sylvain J.","first_name":"Sylvain J."},{"full_name":"Hruska, Martin","last_name":"Hruska","first_name":"Martin"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"last_name":"Dalva","full_name":"Dalva, Matthew B.","first_name":"Matthew B."}],"article_processing_charge":"No","external_id":{"isi":["000459380600001"],"pmid":["30789343"]},"title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","citation":{"short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e41563","volume":8,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7b0800d003f14cd06b1802dea0c52941","file_id":"6098","file_size":7260753,"date_updated":"2020-07-14T12:47:19Z","creator":"dernst","file_name":"2019_eLife_Henderson.pdf","date_created":"2019-03-11T16:15:37Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 8","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SiHi"}],"date_updated":"2023-08-24T14:50:50Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6091"},{"day":"14","publication":"Molecular systems biology","isi":1,"year":"2019","doi":"10.15252/msb.20188470","date_published":"2019-02-14T00:00:00Z","date_created":"2019-02-24T22:59:18Z","quality_controlled":"1","publisher":"Embo Press","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","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.","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","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","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.","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.","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."},"title":"Temporal order and precision of complex stress responses in individual bacteria","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"last_name":"Rieckh","full_name":"Rieckh, Georg","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000459628300003"],"pmid":["30765425"]},"article_number":"e8470","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":15,"issue":"2","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"Bio"}],"month":"02","intvolume":" 15","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425"}],"date_updated":"2023-08-24T14:49:53Z","department":[{"_id":"GaTk"}],"_id":"6046","status":"public","type":"journal_article"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","page":"566-578","date_created":"2019-03-17T22:59:15Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1111/1365-2656.12953","year":"2019","has_accepted_license":"1","isi":1,"publication":"Journal of Animal Ecology","day":"01","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000467994800007"]},"article_processing_charge":"No","author":[{"first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"first_name":"Sophie A.O.","last_name":"Armitage","full_name":"Armitage, Sophie A.O."}],"title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","citation":{"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.","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.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 88","month":"04","abstract":[{"lang":"eng","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"}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"9806","status":"public"}]},"issue":"4","volume":88,"publication_status":"published","publication_identifier":{"issn":["00218790"],"eissn":["13652656"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6107","checksum":"405cde15120de26018b3bd0dfa29986c","date_updated":"2020-07-14T12:47:19Z","file_size":1460662,"creator":"dernst","date_created":"2019-03-18T07:43:06Z","file_name":"2019_JournalAnimalEcology_Kutzer.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"6105","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SyCr"}],"date_updated":"2023-08-25T08:04:53Z","ddc":["570"]},{"isi":1,"year":"2019","day":"04","publication":"Molecular Pharmaceutics","page":"1282-1293","date_published":"2019-03-04T00:00:00Z","doi":"10.1021/acs.molpharmaceut.8b01217","date_created":"2019-03-10T22:59:19Z","publisher":"American Chemical Society","quality_controlled":"1","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Traxl, Alexander","last_name":"Traxl","first_name":"Alexander"},{"first_name":"Severin","last_name":"Mairinger","full_name":"Mairinger, Severin"},{"first_name":"Thomas","last_name":"Filip","full_name":"Filip, Thomas"},{"first_name":"Michael","last_name":"Sauberer","full_name":"Sauberer, Michael"},{"full_name":"Stanek, Johann","last_name":"Stanek","first_name":"Johann"},{"first_name":"Stefan","last_name":"Poschner","full_name":"Poschner, Stefan"},{"first_name":"Walter","full_name":"Jäger, Walter","last_name":"Jäger"},{"last_name":"Zoufal","full_name":"Zoufal, Viktoria","first_name":"Viktoria"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Nicolas","last_name":"Tournier","full_name":"Tournier, Nicolas"},{"last_name":"Bauer","full_name":"Bauer, Martin","first_name":"Martin"},{"first_name":"Thomas","last_name":"Wanek","full_name":"Wanek, Thomas"},{"first_name":"Oliver","last_name":"Langer","full_name":"Langer, Oliver"}],"article_processing_charge":"No","external_id":{"pmid":["30694684"],"isi":["000460600400031"]},"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","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":16,"abstract":[{"lang":"eng","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."}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"03","intvolume":" 16","date_updated":"2023-08-25T08:02:51Z","department":[{"_id":"GaNo"}],"_id":"6088","type":"journal_article","status":"public"},{"date_updated":"2023-08-25T08:02:23Z","department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"_id":"6087","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","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"}]},"issue":"6","volume":176,"ec_funded":1,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"month":"03","intvolume":" 176","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.019","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","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","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","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.","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.","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.","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."},"title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","author":[{"last_name":"Xia","orcid":"0000-0002-5419-7756","full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel J","full_name":"Gütl, Daniel J","last_name":"Gütl"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"external_id":{"pmid":["30773315"],"isi":["000460509600013"]},"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"day":"07","publication":"Cell","isi":1,"year":"2019","date_published":"2019-03-07T00:00:00Z","doi":"10.1016/j.cell.2019.01.019","date_created":"2019-03-10T22:59:19Z","page":"1379-1392.e14","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.).","quality_controlled":"1","publisher":"Elsevier","oa":1},{"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"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.9kj41f0"}],"publisher":"Dryad","month":"02","year":"2019","day":"05","date_created":"2021-08-06T12:06:40Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6105"}]},"doi":"10.5061/dryad.9kj41f0","date_published":"2019-02-05T00:00:00Z","_id":"9806","type":"research_data_reference","status":"public","date_updated":"2023-08-25T08:04:52Z","citation":{"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.","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.","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.","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","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.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","last_name":"Kutzer"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"first_name":"Sophie A.O.","last_name":"Armitage","full_name":"Armitage, Sophie A.O."}],"department":[{"_id":"SyCr"}],"title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 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.","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.","ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098."},"title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","author":[{"full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","last_name":"Sadel","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xu, Disheng","last_name":"Xu","first_name":"Disheng"}],"external_id":{"isi":["000459725600012"],"arxiv":["1601.06118"]},"article_processing_charge":"No","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"day":"01","publication":"Ergodic Theory and Dynamical Systems","isi":1,"year":"2019","date_published":"2019-04-01T00:00:00Z","doi":"10.1017/etds.2017.52","date_created":"2019-03-10T22:59:18Z","page":"1082-1098","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"date_updated":"2023-08-25T08:03:30Z","department":[{"_id":"LaEr"}],"_id":"6086","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":39,"ec_funded":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"04","intvolume":" 39","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.06118"}]},{"issue":"1","volume":8,"publication_identifier":{"eissn":["20477538"],"issn":["20955545"]},"publication_status":"published","file":[{"file_id":"6108","checksum":"d71e528cff9c56f70ccc29dd7005257f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_Light_LeFeber.pdf","date_created":"2019-03-18T08:08:22Z","creator":"dernst","file_size":1119947,"date_updated":"2020-07-14T12:47:19Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 8","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"JoFi"}],"date_updated":"2023-08-25T08:06:10Z","ddc":["530"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6102","doi":"10.1038/s41377-019-0124-3","date_published":"2019-03-06T00:00:00Z","date_created":"2019-03-17T22:59:13Z","has_accepted_license":"1","isi":1,"year":"2019","day":"06","publication":"Light: Science and Applications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"author":[{"last_name":"Le Feber","full_name":"Le Feber, B.","first_name":"B."},{"last_name":"Sipe","full_name":"Sipe, J. E.","first_name":"J. E."},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L.","full_name":"Kuipers, L.","last_name":"Kuipers"},{"last_name":"Rotenberg","full_name":"Rotenberg, N.","first_name":"N."}],"external_id":{"isi":["000460470700004"],"arxiv":["1803.10145"]},"article_processing_charge":"No","title":"A full vectorial mapping of nanophotonic light fields","citation":{"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.","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.","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.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"28"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","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","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.","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.","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."},"title":"Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking","external_id":{"pmid":["30668780"],"isi":["000459634300002"]},"article_processing_charge":"No","author":[{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Agnieszka","last_name":"Bielach","full_name":"Bielach, Agnieszka"},{"first_name":"Prashanth","full_name":"Tamizhselvan, Prashanth","last_name":"Tamizhselvan"},{"full_name":"Madhavan, Sharmila","last_name":"Madhavan","first_name":"Sharmila"},{"last_name":"Ryad","full_name":"Ryad, Eman Elrefaay","first_name":"Eman Elrefaay"},{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"first_name":"Petre","full_name":"Dobrev, Petre","last_name":"Dobrev"},{"first_name":"Radomira","last_name":"Vanková","full_name":"Vanková, Radomira"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Vanesa B.","last_name":"Tognetti","full_name":"Tognetti, Vanesa B."}],"publication":"Plant and Cell Physiology","day":"01","year":"2019","isi":1,"date_created":"2019-03-17T22:59:14Z","date_published":"2019-02-01T00:00:00Z","doi":"10.1093/pcp/pcz001","page":"255-273","publisher":"Oxford University Press","quality_controlled":"1","date_updated":"2023-08-25T08:05:28Z","department":[{"_id":"JiFr"}],"_id":"6104","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"volume":60,"issue":"2","oa_version":"None","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 60","month":"02","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:47:23Z","department":[{"_id":"EdHa"}],"date_updated":"2023-08-25T08:57:30Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6191","issue":"12","related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"volume":116,"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"publication_status":"published","file":[{"date_created":"2019-04-03T14:10:30Z","file_name":"2019_PNAS_Recho.pdf","date_updated":"2020-07-14T12:47:23Z","file_size":3456045,"creator":"dernst","file_id":"6193","checksum":"8b67eee0ea8e5db61583e4d485215258","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 116","abstract":[{"text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"author":[{"last_name":"Recho","full_name":"Recho, Pierre","first_name":"Pierre"},{"full_name":"Hallou, Adrien","last_name":"Hallou","first_name":"Adrien"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"external_id":{"isi":["000461679000027"],"pmid":["30819884"]},"article_processing_charge":"No","title":"Theory of mechanochemical patterning in biphasic biological tissues","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"5344-5349","doi":"10.1073/pnas.1813255116","date_published":"2019-03-19T00:00:00Z","date_created":"2019-03-31T21:59:13Z","has_accepted_license":"1","isi":1,"year":"2019","day":"19","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1},{"isi":1,"year":"2019","day":"01","publication":"Molecular Cancer Research","page":"783-793","doi":"10.1158/1541-7786.MCR-18-0530","date_published":"2019-03-01T00:00:00Z","date_created":"2019-03-31T21:59:12Z","publisher":"AACR","quality_controlled":"1","oa":1,"citation":{"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.","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.","apa":"Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530","ama":"Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Protsyuk, Darya","last_name":"Protsyuk","first_name":"Darya"},{"first_name":"Paul F.","last_name":"Becker","full_name":"Becker, Paul F."},{"last_name":"Stefanescu","full_name":"Stefanescu, Cristina","first_name":"Cristina"},{"first_name":"Christian","full_name":"Gorzelanny, Christian","last_name":"Gorzelanny"},{"first_name":"Jesus F.","last_name":"Glaus Garzon","full_name":"Glaus Garzon, Jesus F."},{"last_name":"Knopfova","full_name":"Knopfova, Lucia","first_name":"Lucia"},{"first_name":"Mathias","full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder"},{"first_name":"Bruno","full_name":"Luckow, Bruno","last_name":"Luckow"},{"first_name":"Stefan W.","last_name":"Schneider","full_name":"Schneider, Stefan W."},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"external_id":{"isi":["000460099800012"],"pmid":["30552233"]},"article_processing_charge":"No","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","publication_identifier":{"issn":["15417786"],"eissn":["15573125"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":17,"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1158/1541-7786.MCR-18-0530","open_access":"1"}],"month":"03","intvolume":" 17","date_updated":"2023-08-25T08:57:01Z","department":[{"_id":"DaSi"}],"_id":"6190","type":"journal_article","article_type":"original","status":"public"},{"scopus_import":"1","month":"03","intvolume":" 8","abstract":[{"lang":"eng","text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies."}],"oa_version":"Published Version","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","relation":"press_release"}]},"volume":8,"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"130d7544b57df4a6787e1263c2d7ea43","file_id":"6293","creator":"dernst","file_size":298466,"date_updated":"2020-07-14T12:47:24Z","file_name":"2019_eLife_Barton.pdf","date_created":"2019-04-11T11:43:38Z"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6230","file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-25T08:59:38Z","ddc":["570"],"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"date_published":"2019-03-21T00:00:00Z","doi":"10.7554/eLife.45380","date_created":"2019-04-07T21:59:15Z","has_accepted_license":"1","isi":1,"year":"2019","day":"21","publication":"eLife","article_number":"e45380","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Hermisson","full_name":"Hermisson, Joachim","first_name":"Joachim"},{"full_name":"Nordborg, Magnus","last_name":"Nordborg","first_name":"Magnus"}],"article_processing_charge":"No","external_id":{"isi":["000461988300001"]},"title":"Why structure matters","citation":{"ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","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).","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"department":[{"_id":"JaMa"}],"date_updated":"2023-08-25T08:59:11Z","type":"journal_article","status":"public","_id":"6232","volume":47,"issue":"2","publication_identifier":{"issn":["00911798"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05364"}],"month":"03","intvolume":" 47","abstract":[{"text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.","lang":"eng"}],"oa_version":"Preprint","author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1705.05364"],"isi":["000459681900005"]},"title":"Boundary regularity of stochastic PDEs","citation":{"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.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","short":"M. Gerencser, Annals of Probability 47 (2019) 804–834.","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"804-834","doi":"10.1214/18-AOP1272","date_published":"2019-03-01T00:00:00Z","date_created":"2019-04-07T21:59:15Z","isi":1,"year":"2019","day":"01","publication":"Annals of Probability","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1},{"quality_controlled":"1","publisher":"Wiley","oa":1,"day":"01","publication":"The Plant Journal","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1111/tpj.14301","date_published":"2019-06-01T00:00:00Z","date_created":"2019-04-09T08:46:44Z","page":"1048-1059","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.","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","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","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.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.","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."},"title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han"},{"first_name":"Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","last_name":"Valošek","full_name":"Valošek, Petr"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["30821050"],"isi":["000473644100008"]},"oa_version":"Published Version","pmid":1,"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."}],"month":"06","intvolume":" 98","scopus_import":"1","file":[{"file_name":"2019_PlantJournal_Rakusov.pdf","date_created":"2019-04-15T09:38:43Z","creator":"dernst","file_size":1383100,"date_updated":"2020-07-14T12:47:25Z","file_id":"6304","checksum":"ad3b5e270b67ba2a45f894ce3be27920","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-313x"],"issn":["0960-7412"]},"publication_status":"published","volume":98,"issue":"6","ec_funded":1,"_id":"6262","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-08-25T10:11:03Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:25Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","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","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","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."},"title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"first_name":"Nouha","full_name":"El Amri, Nouha","last_name":"El Amri"},{"first_name":"Liliane","last_name":"Coche-Guérente","full_name":"Coche-Guérente, Liliane"},{"first_name":"Claude","last_name":"Verdier","full_name":"Verdier, Claude"},{"first_name":"Lionel","full_name":"Bureau, Lionel","last_name":"Bureau"},{"last_name":"Richter","full_name":"Richter, Ralf P.","first_name":"Ralf P."},{"full_name":"Débarre, Delphine","last_name":"Débarre","first_name":"Delphine"}],"external_id":{"isi":["000468707600005"]},"article_processing_charge":"No","day":"01","publication":"Matrix Biology","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-05-01T00:00:00Z","doi":"10.1016/j.matbio.2018.12.002","date_created":"2019-04-11T20:55:01Z","page":"47-59","quality_controlled":"1","publisher":"Elsevier","oa":1,"ddc":["570"],"date_updated":"2023-08-25T10:11:28Z","department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:47:27Z","_id":"6297","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:27Z","file_size":4444339,"date_created":"2020-05-14T09:02:07Z","file_name":"2018_MatrixBiology_Davies.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7825","checksum":"790878cd78bfc54a147ddcc7c8f286a0"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0945-053X"]},"publication_status":"published","volume":"78-79","oa_version":"Submitted 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."}],"month":"05"},{"_id":"6310","status":"public","type":"journal_article","ddc":["512"],"date_updated":"2023-08-25T10:11:55Z","file_date_updated":"2020-07-14T12:47:27Z","department":[{"_id":"TiBr"}],"oa_version":"Submitted Version","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."}],"intvolume":" 349","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"wliqun.pdf","date_created":"2019-04-16T09:12:20Z","file_size":379158,"date_updated":"2020-07-14T12:47:27Z","creator":"tbrownin","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","file_id":"6311","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["00018708"],"eissn":["10902082"]},"volume":349,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 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.","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.","short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.","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"},"title":"Counting rational points on biquadratic hypersurfaces","external_id":{"arxiv":["1810.08426"],"isi":["000468857300025"]},"article_processing_charge":"No","author":[{"last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"full_name":"Hu, L.Q.","last_name":"Hu","first_name":"L.Q."}],"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Advances in Mathematics","day":"20","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-04-16T09:13:25Z","date_published":"2019-06-20T00:00:00Z","doi":"10.1016/j.aim.2019.04.031","page":"920-940"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","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."},"title":"Nitrate modulates the differentiation of root distal stem cells","author":[{"full_name":"Wang, Y","last_name":"Wang","first_name":"Y"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"}],"article_processing_charge":"No","external_id":{"isi":["000466860800010"],"pmid":["30787134"]},"publisher":"ASPB","quality_controlled":"1","oa":1,"day":"01","publication":"Plant Physiology","isi":1,"year":"2019","date_published":"2019-05-01T00:00:00Z","doi":"10.1104/pp.18.01305","date_created":"2019-04-09T08:46:17Z","page":"22-25","_id":"6261","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-08-25T10:10:23Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Nitrate regulation of root stem cell activity is auxin-dependent.","lang":"eng"}],"month":"05","intvolume":" 180","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1104/pp.18.01305","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","volume":180,"issue":"1"},{"date_updated":"2023-08-25T10:14:26Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:47:28Z","_id":"6352","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"publication_status":"published","file":[{"date_created":"2019-04-30T09:52:36Z","file_name":"2019_MolecularBioReport_Temnov.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:28Z","file_size":1948014,"file_id":"6362","checksum":"45bf040bbce1cea274f6013fa18ba21b","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","citation":{"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.","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.","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","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","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov","first_name":"Andrey Alexandrovich"},{"first_name":"Konstantin Arkadevich","last_name":"Rogov","full_name":"Rogov, Konstantin Arkadevich"},{"first_name":"Alla Nikolaevna","full_name":"Sklifas, Alla Nikolaevna","last_name":"Sklifas"},{"first_name":"Elena Valerievna","last_name":"Klychnikova","full_name":"Klychnikova, Elena Valerievna"},{"full_name":"Hartl, Markus","last_name":"Hartl","first_name":"Markus"},{"last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina"},{"id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej","full_name":"Charnagalov, Alexej","last_name":"Charnagalov"}],"external_id":{"isi":["000470332600049"]},"article_processing_charge":"Yes (via OA deal)","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","isi":1,"has_accepted_license":"1","year":"2019","day":"12","publication":"Molecular Biology Reports","date_published":"2019-04-12T00:00:00Z","doi":"10.1007/s11033-019-04765-z","date_created":"2019-04-28T21:59:14Z","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","quality_controlled":"1","publisher":"Springer","oa":1},{"department":[{"_id":"JoFi"}],"date_updated":"2023-08-25T10:15:25Z","type":"journal_article","status":"public","_id":"6348","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-019-1220-5","relation":"erratum"}]},"volume":568,"issue":"7752","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.10608","open_access":"1"}],"month":"04","intvolume":" 568","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."}],"oa_version":"Preprint","author":[{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"last_name":"Leuchs","full_name":"Leuchs, Gerd","first_name":"Gerd"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"article_processing_charge":"No","external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"title":"Resonant electro-optic frequency comb","citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","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.","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","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","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"378-381","doi":"10.1038/s41586-019-1110-x","date_published":"2019-04-18T00:00:00Z","date_created":"2019-04-28T21:59:13Z","isi":1,"year":"2019","day":"18","publication":"Nature","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"2654F984-B435-11E9-9278-68D0E5697425","name":"Interneuro Plasticity During Spatial Learning","grant_number":"I03713"}],"author":[{"last_name":"Stella","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Baracskay","full_name":"Baracskay, Peter"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["30819547"],"isi":["000465169700017"]},"article_processing_charge":"No","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","citation":{"mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.","apa":"Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052","ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.","chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"450-461","doi":"10.1016/j.neuron.2019.01.052","date_published":"2019-04-17T00:00:00Z","date_created":"2019-04-17T08:28:59Z","isi":1,"year":"2019","day":"17","publication":"Neuron","type":"journal_article","article_type":"original","status":"public","_id":"6338","department":[{"_id":"JoCs"}],"date_updated":"2023-08-25T10:13:07Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"month":"04","intvolume":" 102","abstract":[{"text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/","relation":"press_release","description":"News on IST Homepage"}]},"volume":102,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"oa":1,"publisher":"AIP Publishing","quality_controlled":"1","date_created":"2019-01-23T08:35:09Z","doi":"10.1063/1.5058279","date_published":"2019-01-22T00:00:00Z","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","day":"22","year":"2019","isi":1,"article_number":"013122","title":"State space geometry of the chaotic pilot-wave hydrodynamics","external_id":{"isi":["000457409100028"],"arxiv":["1812.09011"]},"article_processing_charge":"No","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"full_name":"Fleury, Marc","last_name":"Fleury","first_name":"Marc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.","apa":"Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279","ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279."},"intvolume":" 29","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.09011"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al.","lang":"eng"}],"issue":"1","related_material":{"link":[{"relation":"erratum","url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157"}]},"volume":29,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"status":"public","type":"journal_article","article_type":"original","_id":"5878","department":[{"_id":"BjHo"}],"date_updated":"2023-08-25T10:16:11Z"},{"_id":"6343","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-25T10:13:31Z","department":[{"_id":"FlSc"}],"abstract":[{"text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 58","month":"10","publication_status":"published","publication_identifier":{"issn":["0959-440X"]},"language":[{"iso":"eng"}],"issue":"10","volume":58,"citation":{"mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” Current Opinion in Structural Biology, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018","chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.","ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000494891800004"]},"article_processing_charge":"No","author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","publisher":"Elsevier","quality_controlled":"1","year":"2019","isi":1,"publication":"Current Opinion in Structural Biology","day":"01","page":"1-9","date_created":"2019-04-19T11:19:13Z","doi":"10.1016/j.sbi.2019.03.018","date_published":"2019-10-01T00:00:00Z"},{"publication_status":"published","publication_identifier":{"isbn":["9781450362825"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"b8e967081e051d1c55ca5d18fb187890","file_id":"8633","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_ACM_Ferrere.pdf","date_created":"2020-10-08T17:25:45Z","file_size":1055421,"date_updated":"2020-10-08T17:25:45Z","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system."}],"oa_version":"Submitted Version","scopus_import":"1","month":"04","date_updated":"2023-08-25T10:19:23Z","ddc":["000"],"file_date_updated":"2020-10-08T17:25:45Z","department":[{"_id":"ToHe"}],"_id":"6428","conference":{"name":"HSCC: Hybrid Systems Computation and Control","end_date":"2019-04-18","location":"Montreal, Canada","start_date":"2019-04-16"},"type":"conference","status":"public","year":"2019","isi":1,"has_accepted_license":"1","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","day":"16","page":"57-66","date_created":"2019-05-13T08:13:46Z","doi":"10.1145/3302504.3311800","date_published":"2019-04-16T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000516713900007"]},"article_processing_charge":"No","author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"last_name":"Ito","full_name":"Ito, Hisahiro","first_name":"Hisahiro"},{"full_name":"Kapinski, James","last_name":"Kapinski","first_name":"James"}],"title":"Interface-aware signal temporal logic","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:47:30Z","date_updated":"2023-08-25T10:18:46Z","ddc":["000","005"],"type":"journal_article","status":"public","_id":"6442","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","relation":"press_release"}]},"volume":38,"issue":"4","ec_funded":1,"publication_status":"published","file":[{"checksum":"1b737dfe3e051aba8f3f4ab1dceda673","file_id":"6443","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-05-14T07:03:55Z","file_name":"2019_ACM_Schreck.pdf","date_updated":"2020-07-14T12:47:30Z","file_size":44328918,"creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 38","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.","lang":"eng"}],"oa_version":"Submitted Version","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck","full_name":"Schreck, Camille"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"external_id":{"isi":["000475740600104"]},"article_processing_charge":"No","title":"Fundamental solutions for water wave animation","citation":{"ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_number":"130","doi":"10.1145/3306346.3323002","date_published":"2019-07-01T00:00:00Z","date_created":"2019-05-14T07:04:06Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"ACM Transactions on Graphics","publisher":"ACM","quality_controlled":"1","oa":1},{"publication_identifier":{"issn":["03019322"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":117,"abstract":[{"lang":"eng","text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"month":"08","intvolume":" 117","date_updated":"2023-08-25T10:19:55Z","department":[{"_id":"BjHo"}],"_id":"6413","article_type":"original","type":"journal_article","status":"public","isi":1,"year":"2019","day":"01","publication":"International Journal of Multiphase Flow","page":"14-24","date_published":"2019-08-01T00:00:00Z","doi":"10.1016/j.ijmultiphaseflow.2019.04.027","date_created":"2019-05-13T07:58:35Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027","apa":"Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Baofang","full_name":"Song, Baofang","last_name":"Song"},{"first_name":"Carlos","full_name":"Plana, Carlos","last_name":"Plana"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"title":"Phase-field simulation of core-annular pipe flow"},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Genetics","day":"10","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-05-13T07:58:38Z","doi":"10.1371/journal.pgen.1008079","date_published":"2019-04-10T00:00:00Z","article_number":"e1008079","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079"},"title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","article_processing_charge":"No","external_id":{"isi":["000466866000029"]},"author":[{"last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dinara R.","full_name":"Usmanova, Dinara R.","last_name":"Usmanova"},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"full_name":"Espinar, Lorena","last_name":"Espinar","first_name":"Lorena"},{"last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"intvolume":" 15","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:30Z","file_size":3726017,"creator":"dernst","date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6445","checksum":"cf3889c8a8a16053dacf9c3776cbe217"}],"publication_status":"published","publication_identifier":{"eissn":["15537404"]},"ec_funded":1,"issue":"4","volume":15,"related_material":{"record":[{"status":"public","id":"9789","relation":"research_data"},{"id":"9790","status":"public","relation":"research_data"},{"relation":"research_data","id":"9797","status":"public"}]},"_id":"6419","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-08-25T10:30:37Z","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:30Z"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2019-05-13T07:58:35Z","date_published":"2019-04-29T00:00:00Z","doi":"10.1038/s41467-019-09628-6","year":"2019","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"29","article_number":"1931","article_processing_charge":"No","external_id":{"isi":["000466118700002"]},"author":[{"full_name":"Moussa, Hagar F.","last_name":"Moussa","first_name":"Hagar F."},{"last_name":"Bsteh","full_name":"Bsteh, Daniel","first_name":"Daniel"},{"full_name":"Yelagandula, Ramesh","last_name":"Yelagandula","first_name":"Ramesh"},{"last_name":"Pribitzer","full_name":"Pribitzer, Carina","first_name":"Carina"},{"full_name":"Stecher, Karin","last_name":"Stecher","first_name":"Karin"},{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bartalska","full_name":"Bartalska, Katarina"},{"full_name":"Michetti, Luca","last_name":"Michetti","first_name":"Luca"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Jorge A.","full_name":"Zepeda-Martinez, Jorge A.","last_name":"Zepeda-Martinez"},{"last_name":"Elling","full_name":"Elling, Ulrich","first_name":"Ulrich"},{"first_name":"Jacob I.","full_name":"Stuckey, Jacob I.","last_name":"Stuckey"},{"full_name":"James, Lindsey I.","last_name":"James","first_name":"Lindsey I."},{"last_name":"Frye","full_name":"Frye, Stephen V.","first_name":"Stephen V."},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","citation":{"mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 10","month":"04","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"oa_version":"Published Version","volume":10,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6550a328335396c856db4cbdda7d2994","file_id":"6448","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1223647,"date_created":"2019-05-14T08:45:51Z","file_name":"2019_NatureComm_Moussa.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"6412","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"SaSi"}],"date_updated":"2023-08-25T10:31:56Z","ddc":["570"]},{"citation":{"chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","ama":"Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011"},"date_updated":"2023-08-25T10:31:31Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000477666000012"]},"article_processing_charge":"No","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"title":"Pathogens and disease defense of invasive ants","department":[{"_id":"SyCr"}],"_id":"6415","type":"journal_article","status":"public","year":"2019","publication_status":"published","isi":1,"publication_identifier":{"eissn":["22145753"],"issn":["22145745"]},"language":[{"iso":"eng"}],"publication":"Current Opinion in Insect Science","day":"01","page":"63-68","date_created":"2019-05-13T07:58:36Z","doi":"10.1016/j.cois.2019.03.011","volume":33,"date_published":"2019-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success."}],"oa_version":"None","quality_controlled":"1","publisher":"Elsevier","scopus_import":"1","intvolume":" 33","month":"06"},{"type":"research_data_reference","status":"public","_id":"9790","article_processing_charge":"No","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva"},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"first_name":"Lucas B.","full_name":"Carey, Lucas B.","last_name":"Carey"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"}],"department":[{"_id":"FyKo"}],"title":"A statistical summary of segment libraries and sequencing results","date_updated":"2023-08-25T10:30:36Z","citation":{"chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. 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Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019."},"status":"public","type":"research_data_reference","_id":"9797","date_created":"2021-08-06T11:08:20Z","doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","related_material":{"record":[{"status":"public","id":"6419","relation":"used_in_publication"}]},"day":"10","year":"2019","month":"04","publisher":"Public Library of Science","oa_version":"Published Version"},{"oa_version":"Published Version","month":"04","publisher":"Public Library of Science","day":"10","year":"2019","related_material":{"record":[{"relation":"used_in_publication","id":"6419","status":"public"}]},"date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s010","date_created":"2021-08-06T08:38:50Z","_id":"9789","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","ieee":"V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010."},"date_updated":"2023-08-25T10:30:36Z","title":"Multiple alignment of His3 orthologues","department":[{"_id":"FyKo"}],"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"last_name":"Espinar","full_name":"Espinar, Lorena","first_name":"Lorena"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"last_name":"Filion","full_name":"Filion, Guillaume J.","first_name":"Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"project":[{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649.","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Bettina","last_name":"Konighofer","full_name":"Konighofer, Bettina"},{"first_name":"Stefan","full_name":"Pranger, Stefan","last_name":"Pranger"}],"external_id":{"isi":["000491468000036"]},"article_processing_charge":"No","title":"Run-time optimization for learned controllers through quantitative games","publisher":"Springer","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"12","publication":"31st International Conference on Computer-Aided Verification","page":"630-649","date_published":"2019-07-12T00:00:00Z","doi":"10.1007/978-3-030-25540-4_36","date_created":"2019-05-16T11:22:30Z","_id":"6462","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","location":"New York, NY, United States","end_date":"2019-07-18","start_date":"2019-07-13"},"status":"public","date_updated":"2023-08-25T10:33:27Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LNCS"],"month":"07","intvolume":" 11561","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c231579f2485c6fd4df17c9443a4d80b","file_id":"6816","creator":"dernst","date_updated":"2020-07-14T12:47:31Z","file_size":659766,"date_created":"2019-08-14T09:35:24Z","file_name":"2019_CAV_Avni.pdf"}],"language":[{"iso":"eng"}],"volume":11561},{"file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"MaSe"}],"ddc":["530"],"date_updated":"2023-08-25T10:37:56Z","status":"public","article_type":"original","type":"journal_article","_id":"6477","volume":91,"issue":"2","file":[{"file_id":"6478","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"RevModPhys.91.021001.pdf","date_created":"2019-05-23T07:39:05Z","file_size":1695677,"date_updated":"2020-07-14T12:47:31Z","creator":"mserbyn"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["0034-6861"],"issn":["1539-0756"]},"publication_status":"published","month":"05","intvolume":" 91","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions."}],"title":"Colloquium: Many-body localization, thermalization, and entanglement","author":[{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"first_name":"Ehud","last_name":"Altman","full_name":"Altman, Ehud"},{"first_name":"Immanuel","full_name":"Bloch, Immanuel","last_name":"Bloch"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.","ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.","ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001","apa":"Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019."},"article_number":"021001","doi":"10.1103/revmodphys.91.021001","date_published":"2019-05-22T00:00:00Z","date_created":"2019-05-23T07:38:43Z","day":"22","publication":"Reviews of Modern Physics","has_accepted_license":"1","isi":1,"year":"2019","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581."},"title":"Breaking down barriers in morning glories","external_id":{"isi":["000474808300001"]},"article_processing_charge":"No","author":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Molecular ecology","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-05-19T21:59:15Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1111/mec.15048","page":"1579-1581","_id":"6466","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["580","576"],"date_updated":"2023-08-25T10:37:30Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:31Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"intvolume":" 28","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"521e3aff3e9263ddf2ffbfe0b6157715","file_id":"6472","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_MolecularEcology_Field.pdf","date_created":"2019-05-20T11:49:06Z","file_size":367711,"date_updated":"2020-07-14T12:47:31Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1365294X"]},"issue":"7","volume":28},{"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"date_created":"2019-05-20T07:33:54Z","file_name":"2019_NatureComm_Chassin.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:31Z","file_size":1191827,"file_id":"6471","checksum":"e214d3e4f8c81e35981583c4569b51b8","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":10,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-023-36111-0"}]},"abstract":[{"text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 10","date_updated":"2023-08-25T10:33:51Z","ddc":["570"],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:31Z","_id":"6465","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Nature Communications","date_published":"2019-05-01T00:00:00Z","doi":"10.1038/s41467-019-09974-5","date_created":"2019-05-19T21:59:14Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5.","ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Chassin, Hélène","last_name":"Chassin","first_name":"Hélène"},{"first_name":"Marius","last_name":"Müller","full_name":"Müller, Marius"},{"last_name":"Tigges","full_name":"Tigges, Marcel","first_name":"Marcel"},{"last_name":"Scheller","full_name":"Scheller, Leo","first_name":"Leo"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz","last_name":"Lang"},{"last_name":"Fussenegger","full_name":"Fussenegger, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"isi":["000466338600006"]},"title":"A modular degron library for synthetic circuits in mammalian cells","article_number":"2013"},{"article_number":"0881","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"article_processing_charge":"No","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John J.","last_name":"Welch","full_name":"Welch, John J."}],"title":"The distribution of epistasis on simple fitness landscapes","oa":1,"quality_controlled":"1","publisher":"Royal Society of London","year":"2019","isi":1,"publication":"Biology Letters","day":"03","date_created":"2019-05-19T21:59:15Z","doi":"10.1098/rsbl.2018.0881","date_published":"2019-04-03T00:00:00Z","_id":"6467","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-25T10:34:41Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"scopus_import":"1","intvolume":" 15","month":"04","publication_status":"published","publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"4","related_material":{"record":[{"id":"9798","status":"public","relation":"research_data"},{"status":"public","id":"9799","relation":"research_data"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}]},"volume":15},{"month":"06","intvolume":" 597","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1113/JP277681"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. "}],"issue":"11","volume":597,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00223751"],"eissn":["14697793"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"6470","department":[{"_id":"GaNo"}],"date_updated":"2023-08-25T10:34:15Z","publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2019-06-01T00:00:00Z","doi":"10.1113/JP277681","date_created":"2019-05-19T21:59:17Z","page":"2925–2947","day":"01","publication":"Journal of Physiology","isi":1,"year":"2019","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","author":[{"first_name":"Tímea","full_name":"Éltes, Tímea","last_name":"Éltes"},{"full_name":"Szoboszlay, Miklos","last_name":"Szoboszlay","first_name":"Miklos"},{"last_name":"Szigeti","full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758","first_name":"Margit Katalin","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nusser, Zoltan","last_name":"Nusser","first_name":"Zoltan"}],"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947."}},{"date_updated":"2023-08-25T10:40:41Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:32Z","_id":"6493","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"New York City, NY, USA","end_date":"2019-07-18","start_date":"2019-07-15","name":"CAV: Computer-Aided Verification"},"type":"conference","keyword":["Synthesis","Linear hybrid automaton","Membership"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-08-14T11:05:30Z","file_name":"2019_CAV_GarciaSoto.pdf","date_updated":"2020-07-14T12:47:32Z","file_size":674795,"creator":"dernst","checksum":"1f1d61b83a151031745ef70a501da3d6","file_id":"6817","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"volume":11561,"abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 11561","month":"07","citation":{"mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000491468000016"]},"article_processing_charge":"No","author":[{"first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam","orcid":"0000−0003−2936−5719"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","last_name":"Zeleznik","full_name":"Zeleznik, Luka"}],"title":"Membership-based synthesis of linear hybrid automata","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"year":"2019","has_accepted_license":"1","isi":1,"publication":"31st International Conference on Computer-Aided Verification","day":"12","page":"297-314","date_created":"2019-05-27T07:09:53Z","doi":"10.1007/978-3-030-25540-4_16","date_published":"2019-07-12T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1"},{"isi":1,"publication_identifier":{"isbn":["9781450362252"]},"year":"2019","publication_status":"published","day":"01","publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","language":[{"iso":"eng"}],"page":"417-418","date_published":"2019-02-01T00:00:00Z","doi":"10.1145/3293883.3297000","date_created":"2019-05-24T10:09:12Z","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"ACM Press","month":"02","date_updated":"2023-08-25T10:41:20Z","citation":{"apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000","ama":"Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019.","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"article_processing_charge":"No","external_id":{"isi":["000587604600044"]},"department":[{"_id":"DaAl"}],"title":"Lock-free channels for programming via communicating sequential processes","_id":"6485","type":"conference_poster","conference":{"name":"PPoPP: Principles and Practice of Parallel Programming","location":"Washington, NY, United States","end_date":"2019-02-20","start_date":"2019-02-16"},"status":"public"},{"abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","month":"10","intvolume":" 224","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6488243334538f5c39099a701cbf76b9","file_id":"8661","success":1,"date_updated":"2020-10-14T08:59:33Z","file_size":1099061,"creator":"dernst","date_created":"2020-10-14T08:59:33Z","file_name":"2019_NewPhytologist_Zhang_accepted.pdf"}],"language":[{"iso":"eng"}],"volume":224,"issue":"2","_id":"6504","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-28T08:40:13Z","ddc":["580"],"file_date_updated":"2020-10-14T08:59:33Z","department":[{"_id":"JiFr"}],"quality_controlled":"1","publisher":"Wiley","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"New Phytologist","page":"761-774","doi":"10.1111/nph.15932","date_published":"2019-10-01T00:00:00Z","date_created":"2019-05-28T14:33:26Z","citation":{"apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"full_name":"He, P","last_name":"He","first_name":"P"},{"first_name":"X","full_name":"Ma, X","last_name":"Ma"},{"full_name":"Yang, Z","last_name":"Yang","first_name":"Z"},{"full_name":"Pang, C","last_name":"Pang","first_name":"C"},{"full_name":"Yu, J","last_name":"Yu","first_name":"J"},{"last_name":"Wang","full_name":"Wang, G","first_name":"G"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, G","last_name":"Xiao","first_name":"G"}],"article_processing_charge":"No","external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"title":"Auxin-mediated statolith production for root gravitropism"},{"_id":"6506","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-28T08:39:47Z","department":[{"_id":"FyKo"}],"abstract":[{"lang":"eng","text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/340828v2"}],"month":"07","intvolume":" 4","publication_identifier":{"issn":["2058-5276"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":4,"issue":"7","citation":{"mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","last_name":"Davidi","first_name":"Dan"},{"first_name":"Elisa","full_name":"Korenblum, Elisa","last_name":"Korenblum"},{"first_name":"Assaf","full_name":"Elazar, Assaf","last_name":"Elazar"},{"first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","last_name":"Putintseva","full_name":"Putintseva, Ekaterina"},{"last_name":"Aharoni","full_name":"Aharoni, Asaph","first_name":"Asaph"},{"full_name":"Tawfik, Dan S.","last_name":"Tawfik","first_name":"Dan S."}],"external_id":{"isi":["000480348200017"]},"article_processing_charge":"No","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"year":"2019","day":"01","publication":"Nature Microbiology","page":"1221–1230","doi":"10.1038/s41564-019-0412-y","date_published":"2019-07-01T00:00:00Z","date_created":"2019-05-29T13:03:30Z"},{"ddc":["570"],"date_updated":"2023-08-28T09:30:57Z","department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:47:33Z","_id":"6521","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:33Z","file_size":1779287,"date_created":"2019-06-08T11:44:20Z","file_name":"2019_Neuroscience_Maes.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6551","checksum":"553c9dbd39727fbed55ee991c51ca4d1"}],"publication_status":"published","publication_identifier":{"issn":["0304-3940"]},"ec_funded":1,"volume":707,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies."}],"intvolume":" 707","month":"08","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310."},"title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","external_id":{"pmid":["31158432"],"isi":["000486094600037"]},"article_processing_charge":"No","author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","last_name":"Colombo","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"last_name":"Schulz","orcid":"0000-0001-5297-733X","full_name":"Schulz, Rouven","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"article_number":"134310","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"publication":"Neuroscience Letters","day":"10","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-06-05T13:16:24Z","date_published":"2019-08-10T00:00:00Z","doi":"10.1016/j.neulet.2019.134310","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","page":"107-111","date_created":"2019-06-02T21:59:14Z","date_published":"2019-06-06T00:00:00Z","doi":"10.1038/s41586-019-1212-5","year":"2019","isi":1,"publication":"Nature","day":"06","external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"article_processing_charge":"No","author":[{"first_name":"Jordi","last_name":"Guiu","full_name":"Guiu, Jordi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Yui, Shiro","last_name":"Yui","first_name":"Shiro"},{"last_name":"Demharter","full_name":"Demharter, Samuel","first_name":"Samuel"},{"first_name":"Svetlana","last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana"},{"first_name":"Martti","last_name":"Maimets","full_name":"Maimets, Martti"},{"last_name":"Jørgensen","full_name":"Jørgensen, Anne","first_name":"Anne"},{"first_name":"Signe","full_name":"Perlman, Signe","last_name":"Perlman"},{"full_name":"Lundvall, Lene","last_name":"Lundvall","first_name":"Lene"},{"full_name":"Mamsen, Linn Salto","last_name":"Mamsen","first_name":"Linn Salto"},{"first_name":"Agnete","last_name":"Larsen","full_name":"Larsen, Agnete"},{"first_name":"Rasmus H.","full_name":"Olesen, Rasmus H.","last_name":"Olesen"},{"last_name":"Andersen","full_name":"Andersen, Claus Yding","first_name":"Claus Yding"},{"first_name":"Lea Langhoff","full_name":"Thuesen, Lea Langhoff","last_name":"Thuesen"},{"first_name":"Kristine Juul","full_name":"Hare, Kristine Juul","last_name":"Hare"},{"full_name":"Pers, Tune H.","last_name":"Pers","first_name":"Tune H."},{"full_name":"Khodosevich, Konstantin","last_name":"Khodosevich","first_name":"Konstantin"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Kim B.","full_name":"Jensen, Kim B.","last_name":"Jensen"}],"title":"Tracing the origin of adult intestinal stem cells","citation":{"ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928","open_access":"1"}],"scopus_import":"1","intvolume":" 570","month":"06","abstract":[{"lang":"eng","text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property."}],"oa_version":"Submitted Version","pmid":1,"volume":570,"publication_status":"published","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"6513","department":[{"_id":"EdHa"}],"date_updated":"2023-08-28T09:30:23Z"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2019-06-16T21:59:14Z","date_published":"2019-08-09T00:00:00Z","doi":"10.1016/j.jmb.2019.05.033","page":"3046-3055","publication":"Journal of Molecular Biology","day":"09","year":"2019","isi":1,"title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","external_id":{"isi":["000482872100002"]},"article_processing_charge":"No","author":[{"last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine"},{"last_name":"Gerrard","full_name":"Gerrard, Elliot J.","first_name":"Elliot J."},{"last_name":"Legrand","full_name":"Legrand, Julien M.D.","first_name":"Julien M.D."},{"first_name":"Robin M.","last_name":"Hobbs","full_name":"Hobbs, Robin M."},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033.","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033."},"intvolume":" 431","month":"08","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/10.1101/583369v1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology."}],"volume":431,"issue":"17","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10898638"],"issn":["00222836"]},"status":"public","article_type":"original","type":"journal_article","_id":"6564","department":[{"_id":"HaJa"}],"date_updated":"2023-08-28T09:39:22Z"},{"publication_identifier":{"issn":["09609822"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"11","volume":29,"abstract":[{"text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). ","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2019.03.035"}],"month":"06","intvolume":" 29","date_updated":"2023-08-28T09:38:00Z","department":[{"_id":"SyCr"}],"_id":"6552","type":"journal_article","article_type":"original","status":"public","isi":1,"year":"2019","day":"03","publication":"Current Biology","page":"R458-R463","doi":"10.1016/j.cub.2019.03.035","date_published":"2019-06-03T00:00:00Z","date_created":"2019-06-09T21:59:10Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.","chicago":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035.","ama":"Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035","apa":"Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035","ieee":"S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","short":"S. Cremer, Current Biology 29 (2019) R458–R463.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"article_processing_charge":"No","external_id":{"isi":["000470902000023"],"pmid":["31163158"]},"title":"Social immunity in insects"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00911798"]},"ec_funded":1,"issue":"3","volume":47,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N)."}],"intvolume":" 47","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05920"}],"scopus_import":"1","date_updated":"2023-08-28T09:32:29Z","department":[{"_id":"LaEr"}],"_id":"6511","status":"public","type":"journal_article","publication":"Annals of Probability","day":"01","year":"2019","isi":1,"date_created":"2019-06-02T21:59:13Z","doi":"10.1214/18-AOP1284","date_published":"2019-05-01T00:00:00Z","page":"1270-1334","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284","ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284.","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284."},"title":"Local single ring theorem on optimal scale","external_id":{"isi":["000466616100003"],"arxiv":["1612.05920"]},"article_processing_charge":"No","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}]},{"author":[{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."}],"article_processing_charge":"No","external_id":{"pmid":["31181348"],"isi":["000486545800014"]},"title":"Multiscale dynamics of branching morphogenesis","citation":{"chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008.","ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 99–105, doi:10.1016/j.ceb.2019.04.008.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.","ieee":"E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019.","apa":"Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008","ama":"Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","page":"99-105","doi":"10.1016/j.ceb.2019.04.008","date_published":"2019-10-01T00:00:00Z","date_created":"2019-06-16T21:59:12Z","isi":1,"year":"2019","day":"01","publication":"Current Opinion in Cell Biology","article_type":"original","type":"journal_article","status":"public","_id":"6559","department":[{"_id":"EdHa"}],"date_updated":"2023-08-28T09:38:57Z","scopus_import":"1","month":"10","intvolume":" 60","abstract":[{"text":"Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":60,"publication_identifier":{"eissn":["18790410"],"issn":["09550674"]},"publication_status":"published","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"06","intvolume":" 13","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication_status":"published","file":[{"file_id":"6644","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-07-16T14:17:09Z","file_name":"2019_ACSNano_Ibanez.pdf","date_updated":"2020-07-14T12:47:33Z","file_size":8628690,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":13,"issue":"6","ec_funded":1,"_id":"6566","article_type":"original","type":"journal_article","status":"public","keyword":["colloidal nanoparticles","asymmetric nanoparticles","inorganic ligands","heterostructures","catalyst assisted growth","nanocomposites","thermoelectrics"],"date_updated":"2023-08-28T12:20:53Z","ddc":["540"],"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"MaIb"}],"quality_controlled":"1","publisher":"American Chemical Society","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"25","publication":"ACS Nano","page":"6572-6580","date_published":"2019-06-25T00:00:00Z","doi":"10.1021/acsnano.9b00346","date_created":"2019-06-18T13:54:34Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"mla":"Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano, vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346.","short":"M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580.","ieee":"M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks,” ACS Nano, vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019.","apa":"Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., … Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b00346","ama":"Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346","chicago":"Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical Society, 2019. https://doi.org/10.1021/acsnano.9b00346.","ista":"Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la, Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 13(6), 6572–6580."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"last_name":"Genç","full_name":"Genç, Aziz","first_name":"Aziz"},{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oleksandr","last_name":"Dobrozhan","full_name":"Dobrozhan, Oleksandr"},{"first_name":"Olga","last_name":"Nazarenko","full_name":"Nazarenko, Olga"},{"full_name":"Mata, María de la","last_name":"Mata","first_name":"María de la"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"},{"last_name":"Kovalenko","full_name":"Kovalenko, Maksym V.","first_name":"Maksym V."}],"external_id":{"pmid":["31185159"],"isi":["000473248300043"]},"article_processing_charge":"Yes (in subscription journal)","title":"Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks"},{"ddc":["576"],"date_updated":"2023-08-28T12:26:51Z","file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"PreCl"}],"_id":"6607","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_name":"nature_2019_Nguyen.pdf","date_created":"2019-07-08T15:15:28Z","creator":"kschuh","file_size":2017352,"date_updated":"2020-07-14T12:47:34Z","file_id":"6623","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","volume":9,"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically."}],"intvolume":" 9","month":"06","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139.","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0","apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0","short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019).","ieee":"C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0."},"title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","article_processing_charge":"No","external_id":{"isi":["000472597400042"]},"author":[{"last_name":"Nguyen","full_name":"Nguyen, Chi Huu","first_name":"Chi Huu"},{"last_name":"Glüxam","full_name":"Glüxam, Tobias","first_name":"Tobias"},{"first_name":"Angela","last_name":"Schlerka","full_name":"Schlerka, Angela"},{"full_name":"Bauer, Katharina","last_name":"Bauer","id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina"},{"first_name":"Alexander M.","full_name":"Grandits, Alexander M.","last_name":"Grandits"},{"first_name":"Hubert","full_name":"Hackl, Hubert","last_name":"Hackl"},{"last_name":"Dovey","full_name":"Dovey, Oliver","first_name":"Oliver"},{"first_name":"Sabine","last_name":"Zöchbauer-Müller","full_name":"Zöchbauer-Müller, Sabine"},{"last_name":"Cooper","full_name":"Cooper, Jonathan L.","first_name":"Jonathan L."},{"full_name":"Vassiliou, George S.","last_name":"Vassiliou","first_name":"George S."},{"first_name":"Dagmar","last_name":"Stoiber","full_name":"Stoiber, Dagmar"},{"last_name":"Wieser","full_name":"Wieser, Rotraud","first_name":"Rotraud"},{"full_name":"Heller, Gerwin","last_name":"Heller","first_name":"Gerwin"}],"article_number":"9139","publication":"Scientific Reports","day":"24","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-07-07T21:59:19Z","doi":"10.1038/s41598-019-45579-0","date_published":"2019-06-24T00:00:00Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1"},{"volume":570,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.05865"}],"month":"06","intvolume":" 570","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"JoFi"}],"date_updated":"2023-08-28T12:29:56Z","type":"journal_article","status":"public","_id":"6609","page":"480-483","date_published":"2019-06-27T00:00:00Z","doi":"10.1038/s41586-019-1320-2","date_created":"2019-07-07T21:59:20Z","isi":1,"year":"2019","day":"27","publication":"Nature","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dylan","last_name":"Lewis","full_name":"Lewis, Dylan"},{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","last_name":"Arnold"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"external_id":{"arxiv":["1809.05865"],"isi":["000472860000042"]},"article_processing_charge":"No","title":"Stationary entangled radiation from micromechanical motion","citation":{"ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” Nature. Nature Publishing Group, 2019. https://doi.org/10.1038/s41586-019-1320-2.","short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483.","ieee":"S. Barzanjeh et al., “Stationary entangled radiation from micromechanical motion,” Nature, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., & Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-019-1320-2","ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. Nature. 2019;570:480-483. doi:10.1038/s41586-019-1320-2","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” Nature, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:10.1038/s41586-019-1320-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}]},{"citation":{"ista":"Shehu Y. 2019. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138.","chicago":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics. Springer, 2019. https://doi.org/10.1007/s00025-019-1061-4.","apa":"Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. Springer. https://doi.org/10.1007/s00025-019-1061-4","ama":"Shehu Y. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 2019;74(4). doi:10.1007/s00025-019-1061-4","ieee":"Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces,” Results in Mathematics, vol. 74, no. 4. Springer, 2019.","short":"Y. Shehu, Results in Mathematics 74 (2019).","mla":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics, vol. 74, no. 4, 138, Springer, 2019, doi:10.1007/s00025-019-1061-4."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2101.09068"],"isi":["000473237500002"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","last_name":"Shehu"}],"title":"Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces","article_number":"138","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"year":"2019","has_accepted_license":"1","isi":1,"publication":"Results in Mathematics","day":"01","date_created":"2019-06-29T10:11:30Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1007/s00025-019-1061-4","oa":1,"quality_controlled":"1","publisher":"Springer","date_updated":"2023-08-28T12:26:22Z","ddc":["000"],"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:34Z","_id":"6596","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1420-9012"],"issn":["1422-6383"]},"language":[{"iso":"eng"}],"file":[{"checksum":"c6d18cb1e16fc0c36a0e0f30b4ebbc2d","file_id":"6605","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Springer_2019_Shehu.pdf","date_created":"2019-07-03T15:20:40Z","creator":"kschuh","file_size":466942,"date_updated":"2020-07-14T12:47:34Z"}],"ec_funded":1,"issue":"4","volume":74,"abstract":[{"lang":"eng","text":"It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 74","month":"12"},{"_id":"6601","type":"journal_article","article_type":"review","status":"public","date_updated":"2023-08-28T12:25:21Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"scopus_import":"1","intvolume":" 178","month":"07","publication_status":"published","publication_identifier":{"issn":["00928674"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","volume":178,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052.","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000473002700005"],"pmid":["31251912"]},"author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"Mechanochemical feedback loops in development and disease","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2019","isi":1,"publication":"Cell","day":"27","page":"12-25","date_created":"2019-06-30T21:59:11Z","doi":"10.1016/j.cell.2019.05.052","date_published":"2019-07-27T00:00:00Z"},{"_id":"6617","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["500"],"date_updated":"2023-08-28T12:31:21Z","department":[{"_id":"JuFi"}],"file_date_updated":"2020-07-14T12:47:34Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably."}],"intvolume":" 234","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"6626","checksum":"4cff75fa6addb0770991ad9c474ab404","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-08T15:56:47Z","file_name":"Springer_2019_Fischer.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:34Z","file_size":1377659}],"publication_status":"published","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"volume":234,"issue":"2","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Fischer, J. L. (2019). The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w","ama":"Fischer JL. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 2019;234(2):635–726. doi:10.1007/s00205-019-01400-w","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726.","ieee":"J. L. Fischer, “The choice of representative volumes in the approximation of effective properties of random materials,” Archive for Rational Mechanics and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019.","mla":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w.","ista":"Fischer JL. 2019. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 234(2), 635–726.","chicago":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w."},"title":"The choice of representative volumes in the approximation of effective properties of random materials","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1807.00834"],"isi":["000482386000006"]},"author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer"}],"oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Archive for Rational Mechanics and Analysis","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-07-07T21:59:23Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1007/s00205-019-01400-w","page":"635–726"},{"author":[{"last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000475301500018"],"pmid":["31181636"]},"title":"PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton","citation":{"chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules. MDPI, 2019. https://doi.org/10.3390/biom9060222.","ista":"Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222.","mla":"Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019, doi:10.3390/biom9060222.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6. MDPI, 2019.","short":"M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019).","ama":"Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222","apa":"Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. MDPI. https://doi.org/10.3390/biom9060222"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_number":"222","date_published":"2019-06-07T00:00:00Z","doi":"10.3390/biom9060222","date_created":"2019-07-07T21:59:21Z","has_accepted_license":"1","isi":1,"year":"2019","day":"07","publication":"Biomolecules","publisher":"MDPI","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"date_updated":"2023-08-28T12:30:24Z","ddc":["580"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6611","issue":"6","volume":9,"ec_funded":1,"publication_status":"published","file":[{"file_name":"biomolecules-2019-Matous.pdf","date_created":"2019-07-08T15:46:32Z","file_size":1066773,"date_updated":"2020-07-14T12:47:34Z","creator":"kschuh","checksum":"1ce1bd36038fe5381057a1bcc6760083","file_id":"6625","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 9","abstract":[{"text":"Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version"},{"date_created":"2019-07-07T21:59:25Z","doi":"10.1007/s11425-018-9543-8","date_published":"2019-12-01T00:00:00Z","page":"2435–2446","publication":"Science China Mathematics","day":"01","year":"2019","isi":1,"oa":1,"publisher":"Springer","quality_controlled":"1","title":"On a certain non-split cubic surface","external_id":{"isi":["000509102200001"],"arxiv":["1709.09476"]},"article_processing_charge":"No","author":[{"first_name":"Régis","last_name":"De La Bretèche","full_name":"De La Bretèche, Régis"},{"full_name":"Destagnol, Kevin N","last_name":"Destagnol","id":"44DDECBC-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin N"},{"first_name":"Jianya","last_name":"Liu","full_name":"Liu, Jianya"},{"first_name":"Jie","full_name":"Wu, Jie","last_name":"Wu"},{"first_name":"Yongqiang","full_name":"Zhao, Yongqiang","last_name":"Zhao"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics. Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8.","ista":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split cubic surface. Science China Mathematics. 62(12), 2435–2446.","mla":"De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8.","ama":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8","apa":"De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019). On a certain non-split cubic surface. Science China Mathematics. Springer. https://doi.org/10.1007/s11425-018-9543-8","ieee":"R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer, pp. 2435–2446, 2019.","short":"R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China Mathematics 62 (2019) 2435–2446."},"volume":62,"issue":"12","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["16747283"]},"intvolume":" 62","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09476"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures.\r\n","lang":"eng"}],"department":[{"_id":"TiBr"}],"date_updated":"2023-08-28T12:32:20Z","status":"public","article_type":"original","type":"journal_article","_id":"6620"},{"publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","page":"1356-1374","doi":"10.1111/evo.13784","date_published":"2019-07-01T00:00:00Z","date_created":"2019-07-14T21:59:20Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Evolution","project":[{"_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"704172","name":"Rate of Adaptation in Changing Environment"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova"},{"first_name":"Martin ","full_name":"Krejca, Martin ","last_name":"Krejca"},{"first_name":"Per Kristian","full_name":"Lehre, Per Kristian","last_name":"Lehre"},{"first_name":"Timo","last_name":"Kötzing","full_name":"Kötzing, Timo"}],"external_id":{"isi":["000474031600001"]},"article_processing_charge":"Yes (via OA deal)","title":"Surfing on the seascape: Adaptation in a changing environment","citation":{"mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"07","intvolume":" 73","abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"oa_version":"Published Version","issue":"7","volume":73,"ec_funded":1,"publication_status":"published","file":[{"checksum":"9831ca65def2d62498c7b08338b6d237","file_id":"6643","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-16T06:08:31Z","file_name":"2019_Evolution_TrubenovaBarbora.pdf","creator":"apreinsp","date_updated":"2020-07-14T12:47:34Z","file_size":815416}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"6637","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:34Z","date_updated":"2023-08-29T06:31:14Z","ddc":["576"]},{"status":"public","type":"journal_article","_id":"6634","department":[{"_id":"HeEd"}],"date_updated":"2023-08-29T06:32:48Z","month":"06","intvolume":" 53","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.06926"}],"oa_version":"Preprint","abstract":[{"text":"In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure.","lang":"eng"}],"issue":"2","volume":53,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Lower and upper bounds for the waists of different spaces","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hubard","full_name":"Hubard, Alfredo","first_name":"Alfredo"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"article_processing_charge":"No","external_id":{"isi":["000472541600004"],"arxiv":["1612.06926"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis 53 (2019) 457–490.","ieee":"A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53, no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019.","ama":"Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490. doi:10.12775/TMNA.2019.008","apa":"Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008","mla":"Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008.","ista":"Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490.","chicago":"Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008."},"publisher":"Akademicka Platforma Czasopism","quality_controlled":"1","oa":1,"date_published":"2019-06-01T00:00:00Z","doi":"10.12775/TMNA.2019.008","date_created":"2019-07-14T21:59:19Z","page":"457-490","day":"01","publication":"Topological Methods in Nonlinear Analysis","isi":1,"year":"2019"},{"department":[{"_id":"UlWa"}],"date_updated":"2023-08-29T06:31:41Z","type":"journal_article","status":"public","_id":"6638","ec_funded":1,"volume":342,"issue":"11","publication_status":"published","publication_identifier":{"issn":["0012-365X"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1901.09955","open_access":"1"}],"scopus_import":"1","intvolume":" 342","month":"11","abstract":[{"lang":"eng","text":"The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one."}],"oa_version":"Preprint","external_id":{"isi":["000486358100025"],"arxiv":["1901.09955"]},"article_processing_charge":"No","author":[{"first_name":"André ","last_name":"Silva","full_name":"Silva, André "},{"last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bruce","last_name":"Richter","full_name":"Richter, Bruce"},{"first_name":"Orlando","full_name":"Lee, Orlando","last_name":"Lee"}],"title":"Graphs with at most one crossing","citation":{"short":"A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342 (2019) 3201–3207.","ieee":"A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207, 2019.","apa":"Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031","ama":"Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing. Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031","mla":"Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics, vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031.","ista":"Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one crossing. Discrete Mathematics. 342(11), 3201–3207.","chicago":"Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"page":"3201-3207","date_created":"2019-07-14T21:59:20Z","doi":"10.1016/j.disc.2019.06.031","date_published":"2019-11-01T00:00:00Z","year":"2019","isi":1,"publication":"Discrete Mathematics","day":"01","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"month":"10","intvolume":" 60","publisher":"Elsevier","scopus_import":"1","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis."}],"doi":"10.1016/j.ceb.2019.05.007","volume":60,"date_published":"2019-10-01T00:00:00Z","date_created":"2019-07-14T21:59:17Z","page":"114-120","day":"01","language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","publication_identifier":{"issn":["0955-0674"]},"isi":1,"year":"2019","publication_status":"published","status":"public","type":"journal_article","_id":"6631","title":"Cell division and tissue mechanics","department":[{"_id":"CaHe"}],"author":[{"id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","last_name":"Godard","full_name":"Godard, Benoit G"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"isi":["000486545800016"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-29T06:33:14Z","citation":{"ista":"Godard BG, Heisenberg C-PJ. 2019. Cell division and tissue mechanics. Current Opinion in Cell Biology. 60, 114–120.","chicago":"Godard, Benoit G, and Carl-Philipp J Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.05.007.","ama":"Godard BG, Heisenberg C-PJ. Cell division and tissue mechanics. Current Opinion in Cell Biology. 2019;60:114-120. doi:10.1016/j.ceb.2019.05.007","apa":"Godard, B. G., & Heisenberg, C.-P. J. (2019). Cell division and tissue mechanics. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.05.007","ieee":"B. G. Godard and C.-P. J. Heisenberg, “Cell division and tissue mechanics,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 114–120, 2019.","short":"B.G. Godard, C.-P.J. Heisenberg, Current Opinion in Cell Biology 60 (2019) 114–120.","mla":"Godard, Benoit G., and Carl-Philipp J. Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 114–20, doi:10.1016/j.ceb.2019.05.007."}},{"date_updated":"2023-08-29T06:40:49Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:36Z","department":[{"_id":"BeBi"}],"_id":"6660","type":"journal_article","status":"public","publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","file":[{"file_size":10109800,"date_updated":"2020-07-14T12:47:36Z","creator":"dernst","file_name":"2019_ACM_Sumin_AuthorVersion.pdf","date_created":"2019-07-24T07:36:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6669","checksum":"43c2019d6b48ed9c56e31686c4c2d1f5"},{"checksum":"f80f365a04e35855fa467ea7ab26b16c","file_id":"6938","access_level":"open_access","relation":"supplementary_material","content_type":"application/zip","date_created":"2019-10-11T06:51:07Z","file_name":"sumin19geometry-aware-suppl.zip","creator":"dernst","date_updated":"2020-07-14T12:47:36Z","file_size":11051245}],"language":[{"iso":"eng"}],"volume":38,"issue":"4","ec_funded":1,"abstract":[{"lang":"eng","text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers."}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 38","citation":{"ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992","apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992","short":"D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.","ista":"Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111.","chicago":"Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Denis","last_name":"Sumin","full_name":"Sumin, Denis"},{"last_name":"Weyrich","full_name":"Weyrich, Tim","first_name":"Tim"},{"full_name":"Rittig, Tobias","last_name":"Rittig","first_name":"Tobias"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"first_name":"Thomas","full_name":"Nindel, Thomas","last_name":"Nindel"},{"last_name":"Wilkie","full_name":"Wilkie, Alexander","first_name":"Alexander"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"}],"article_processing_charge":"No","external_id":{"isi":["000475740600085"]},"title":"Geometry-aware scattering compensation for 3D printing","article_number":"111","project":[{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","grant_number":"642841"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"isi":1,"has_accepted_license":"1","year":"2019","day":"04","publication":"ACM Transactions on Graphics","doi":"10.1145/3306346.3322992","date_published":"2019-07-04T00:00:00Z","date_created":"2019-07-22T07:22:28Z","quality_controlled":"1","publisher":"ACM","oa":1},{"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:35Z","date_updated":"2023-08-29T06:35:05Z","ddc":["576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"6658","issue":"7","volume":29,"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","file":[{"creator":"apreinsp","date_updated":"2020-07-14T12:47:35Z","file_size":2319022,"date_created":"2019-07-24T08:05:56Z","file_name":"2019_GenomeResearch_Raices.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6670","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 29","abstract":[{"text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. ","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Raices","full_name":"Raices, Julia"},{"full_name":"Otto, Paulo","last_name":"Otto","first_name":"Paulo"},{"first_name":"Maria","full_name":"Vibranovski, Maria","last_name":"Vibranovski"}],"external_id":{"isi":["000473730600007"]},"article_processing_charge":"No","title":"Haploid selection drives new gene male germline expression","citation":{"chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118.","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019.","ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118","apa":"Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"1115-1122","doi":"10.1101/gr.238824.118","date_published":"2019-07-01T00:00:00Z","date_created":"2019-07-21T21:59:15Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Genome Research","publisher":"CSH Press","quality_controlled":"1","oa":1},{"publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b4562af94672b44d2a501046427412af","file_id":"6651","creator":"dernst","file_size":74316182,"date_updated":"2020-07-14T12:47:35Z","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","date_created":"2019-07-19T06:18:53Z"}],"language":[{"iso":"eng"}],"issue":"4","volume":38,"related_material":{"link":[{"url":"https://youtu.be/SO349S8-x_w","relation":"supplementary_material","description":"YouTube Video"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry."}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 38","date_updated":"2023-08-29T06:35:52Z","ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:35Z","_id":"6650","type":"journal_article","status":"public","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"ACM Transactions on Graphics","date_published":"2019-07-01T00:00:00Z","doi":"10.1145/3306346.3322981","date_created":"2019-07-19T06:18:15Z","quality_controlled":"1","publisher":"ACM","oa":1,"citation":{"mla":"Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981.","ieee":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","apa":"Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981","ama":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.","ista":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","full_name":"Malomo, Luigi","last_name":"Malomo"},{"full_name":"Giorgi, Daniela","last_name":"Giorgi","first_name":"Daniela"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"}],"article_processing_charge":"No","external_id":{"isi":["000475740600084"]},"title":"Volume-aware design of composite molds","article_number":"110","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}]},{"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"article_number":"1171","author":[{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"first_name":"Stephen T.","full_name":"Abedon, Stephen T.","last_name":"Abedon"}],"external_id":{"isi":["000470131200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","citation":{"ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Frontiers","oa":1,"doi":"10.3389/fmicb.2019.01171","date_published":"2019-06-03T00:00:00Z","date_created":"2019-07-28T21:59:18Z","has_accepted_license":"1","isi":1,"year":"2019","day":"03","publication":"Frontiers in Microbiology","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6717","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:38Z","date_updated":"2023-08-29T06:41:20Z","ddc":["570"],"scopus_import":"1","month":"06","intvolume":" 10","abstract":[{"text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple.","lang":"eng"}],"oa_version":"Published Version","volume":10,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"317a06067e9a8e717bb55f23e0d77ba7","file_id":"6722","date_updated":"2020-07-14T12:47:38Z","file_size":246151,"creator":"apreinsp","date_created":"2019-07-29T07:51:54Z","file_name":"2019_Frontiers_Igler.pdf"}],"language":[{"iso":"eng"}]},{"_id":"6680","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-29T06:43:58Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:37Z","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 73","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","file":[{"checksum":"772ce7035965153959b946a1033de1ca","file_id":"6881","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_Evolution_Sachdeva.pdf","date_created":"2019-09-17T10:56:27Z","file_size":937573,"date_updated":"2020-07-14T12:47:37Z","creator":"kschuh"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9802","status":"public","relation":"research_data"}]},"volume":73,"issue":"9","citation":{"ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"external_id":{"isi":["000481300600001"]},"article_processing_charge":"Yes (via OA deal)","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","publisher":"Wiley","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Evolution","page":"1729-1745","doi":"10.1111/evo.13812","date_published":"2019-09-01T00:00:00Z","date_created":"2019-07-25T09:08:28Z"},{"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","article_processing_charge":"No","external_id":{"pmid":["30289430"],"isi":["000493043500004"]},"author":[{"last_name":"Cossard","full_name":"Cossard, Guillaume","first_name":"Guillaume"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"last_name":"Pannell","full_name":"Pannell, John ","first_name":"John "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183.","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131.","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.","apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019."},"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2019-07-28T21:59:15Z","doi":"10.1093/aob/mcy183","date_published":"2019-06-04T00:00:00Z","page":"1119-1131","publication":"Annals of botany","day":"04","year":"2019","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"6710","department":[{"_id":"BeVi"}],"date_updated":"2023-08-29T06:42:22Z","intvolume":" 123","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species."}],"issue":"7","volume":123,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-8290"],"issn":["0305-7364"]}},{"type":"research_data_reference","status":"public","_id":"9804","article_processing_charge":"No","author":[{"last_name":"Castro","full_name":"Castro, João Pl","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"first_name":"Marta","full_name":"Marchini, Marta","last_name":"Marchini"},{"orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"last_name":"Kučka","full_name":"Kučka, Marek","first_name":"Marek"},{"first_name":"William H.","full_name":"Beluch, William H.","last_name":"Beluch"},{"last_name":"Naumann","full_name":"Naumann, Ronald","first_name":"Ronald"},{"last_name":"Skuplik","full_name":"Skuplik, Isabella","first_name":"Isabella"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"}],"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","department":[{"_id":"NiBa"}],"date_updated":"2023-08-29T06:41:51Z","citation":{"ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"oa":1,"publisher":"Dryad","month":"06","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"oa_version":"Published Version","date_created":"2021-08-06T11:52:54Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]},"date_published":"2019-06-06T00:00:00Z","doi":"10.5061/dryad.0q2h6tk","year":"2019","day":"06"},{"publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"oa":1,"month":"07","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"oa_version":"Published Version","related_material":{"record":[{"id":"6680","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.8tp0900","date_published":"2019-07-16T00:00:00Z","date_created":"2021-08-06T11:45:11Z","year":"2019","day":"16","type":"research_data_reference","status":"public","_id":"9802","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"}],"article_processing_charge":"No","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","department":[{"_id":"NiBa"}],"date_updated":"2023-08-29T06:43:57Z","citation":{"short":"H. Sachdeva, (2019).","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"oa_version":"Published Version","abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"intvolume":" 627","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"83b9209ed9eefbdcefd89019c5a97805","file_id":"6766","creator":"dernst","date_updated":"2020-07-14T12:47:39Z","file_size":14420451,"date_created":"2019-08-05T08:08:59Z","file_name":"2019_AstronomyAstrophysics_Pranav.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["14320746"],"issn":["00046361"]},"volume":627,"_id":"6756","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["520","530"],"date_updated":"2023-08-29T07:01:48Z","file_date_updated":"2020-07-14T12:47:39Z","department":[{"_id":"HeEd"}],"oa":1,"quality_controlled":"1","publisher":"EDP Sciences","publication":"Astronomy and Astrophysics","day":"17","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-08-04T21:59:18Z","doi":"10.1051/0004-6361/201834916","date_published":"2019-07-17T00:00:00Z","article_number":"A163","project":[{"name":"Toward Computational Information Topology","grant_number":"M62909-18-1-2038","_id":"265683E4-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019.","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834916","ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 2019;627. doi:10.1051/0004-6361/201834916","mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics, vol. 627, A163, EDP Sciences, 2019, doi:10.1051/0004-6361/201834916.","ista":"Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.","chicago":"Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834916."},"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","article_processing_charge":"No","external_id":{"isi":["000475839300003"],"arxiv":["1812.07678"]},"author":[{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"full_name":"Adler, Robert J.","last_name":"Adler","first_name":"Robert J."},{"first_name":"Thomas","full_name":"Buchert, Thomas","last_name":"Buchert"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Jones, Bernard J.T.","last_name":"Jones","first_name":"Bernard J.T."},{"first_name":"Armin","last_name":"Schwartzman","full_name":"Schwartzman, Armin"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rien","last_name":"Van De Weygaert","full_name":"Van De Weygaert, Rien"}]},{"date_updated":"2023-08-29T06:53:58Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:39Z","_id":"6755","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6765","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_size":580205,"date_updated":"2020-07-14T12:47:39Z","creator":"dernst","file_name":"2019_GenomeBiology_Picard.pdf","date_created":"2019-08-05T07:55:02Z"}],"volume":11,"issue":"7","acknowledged_ssus":[{"_id":"CampIT"}],"abstract":[{"text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 11","month":"07","citation":{"ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford Academic Press. https://doi.org/10.1093/gbe/evz133","ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford Academic Press, 2019. https://doi.org/10.1093/gbe/evz133."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"author":[{"first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"first_name":"David","last_name":"Roquis","full_name":"Roquis, David"},{"first_name":"Ingo","full_name":"Bulla, Ingo","last_name":"Bulla"},{"full_name":"Augusto, Ronaldo C.","last_name":"Augusto","first_name":"Ronaldo C."},{"full_name":"Arancibia, Nathalie","last_name":"Arancibia","first_name":"Nathalie"},{"last_name":"Grunau","full_name":"Grunau, Christoph","first_name":"Christoph"},{"last_name":"Boissier","full_name":"Boissier, Jérôme","first_name":"Jérôme"},{"full_name":"Cosseau, Céline","last_name":"Cosseau","first_name":"Céline"}],"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","year":"2019","has_accepted_license":"1","isi":1,"publication":"Genome biology and evolution","day":"01","page":"1909-1922","date_created":"2019-08-04T21:59:18Z","doi":"10.1093/gbe/evz133","date_published":"2019-07-01T00:00:00Z","oa":1,"publisher":"Oxford Academic Press","quality_controlled":"1"}]