[{"citation":{"ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.","ieee":"F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Immler","full_name":"Immler, Fabian","first_name":"Fabian"},{"full_name":"Althoff, Matthias","last_name":"Althoff","first_name":"Matthias"},{"first_name":"Luis","full_name":"Benet, Luis","last_name":"Benet"},{"last_name":"Chapoutot","full_name":"Chapoutot, Alexandre","first_name":"Alexandre"},{"last_name":"Chen","full_name":"Chen, Xin","first_name":"Xin"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"first_name":"Luca","last_name":"Geretti","full_name":"Geretti, Luca"},{"last_name":"Kochdumper","full_name":"Kochdumper, Niklas","first_name":"Niklas"},{"full_name":"Sanders, David P.","last_name":"Sanders","first_name":"David P."},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"article_processing_charge":"No","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","publisher":"EasyChair Publications","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2019","day":"25","publication":"EPiC Series in Computing","page":"41-61","date_published":"2019-05-25T00:00:00Z","doi":"10.29007/m75b","date_created":"2020-03-08T23:00:49Z","_id":"7576","type":"conference","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","location":"Montreal, Canada","end_date":"2019-04-15","start_date":"2019-04-15"},"status":"public","date_updated":"2021-01-12T08:14:17Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:48:00Z","abstract":[{"text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"05","intvolume":" 61","publication_identifier":{"eissn":["23987340"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9138977a06fcd6a95976eb4bca875f0c","file_id":"7617","creator":"dernst","file_size":1934830,"date_updated":"2020-07-14T12:48:00Z","file_name":"2019_ARCH19_Immler.pdf","date_created":"2020-03-24T07:36:36Z"}],"language":[{"iso":"eng"}],"volume":61},{"language":[{"iso":"eng"}],"day":"26","publication_status":"submitted","year":"2019","date_created":"2020-04-01T10:10:21Z","date_published":"2019-12-26T00:00:00Z","page":"50","oa_version":"Preprint","abstract":[{"text":"Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and beyond. ","lang":"eng"}],"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775.v1"}],"oa":1,"publisher":"ChemRxiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv, n.d.","ista":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.","mla":"Prehal, Christian, et al. A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering. ChemRxiv.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, (n.d.).","ieee":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S. A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.” ChemRxiv.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. ChemRxiv.","ama":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering."},"date_updated":"2020-04-06T10:36:21Z","title":"A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering","article_processing_charge":"No","author":[{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"last_name":"Samojlov","full_name":"Samojlov, Aleksej","first_name":"Aleksej"},{"last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred","first_name":"Manfred"},{"first_name":"Manfred","full_name":"Kriechbaum, Manfred","last_name":"Kriechbaum"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"_id":"7627","status":"public","type":"preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y.","ista":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436.","mla":"Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y.","ieee":"O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” Nature Communications, vol. 10. Springer Nature, 2019.","short":"O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019).","apa":"Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y","ama":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nature Communications. 2019;10. doi:10.1038/s41467-019-13225-y"},"date_updated":"2021-01-12T08:15:01Z","title":"Accurate, scalable and integrative haplotype estimation","article_processing_charge":"No","author":[{"full_name":"Delaneau, Olivier","last_name":"Delaneau","first_name":"Olivier"},{"full_name":"Zagury, Jean-François","last_name":"Zagury","first_name":"Jean-François"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"first_name":"Jonathan L.","full_name":"Marchini, Jonathan L.","last_name":"Marchini"},{"first_name":"Emmanouil T.","last_name":"Dermitzakis","full_name":"Dermitzakis, Emmanouil T."}],"article_number":"5436","_id":"7710","status":"public","article_type":"original","type":"journal_article","publication":"Nature Communications","language":[{"iso":"eng"}],"day":"28","publication_status":"published","year":"2019","publication_identifier":{"issn":["2041-1723"]},"date_created":"2020-04-30T10:40:32Z","doi":"10.1038/s41467-019-13225-y","volume":10,"date_published":"2019-11-28T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.","lang":"eng"}],"intvolume":" 10","month":"11","oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-019-13225-y","open_access":"1"}],"publisher":"Springer Nature","quality_controlled":"1"},{"_id":"7711","article_type":"original","type":"journal_article","status":"public","citation":{"chicago":"Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.","mla":"Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.","ieee":"R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019."},"date_updated":"2021-01-12T08:15:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"last_name":"Bevers","full_name":"Bevers, Roel P. J.","first_name":"Roel P. J."},{"full_name":"Litovchenko, Maria","last_name":"Litovchenko","first_name":"Maria"},{"first_name":"Adamandia","last_name":"Kapopoulou","full_name":"Kapopoulou, Adamandia"},{"full_name":"Braman, Virginie S.","last_name":"Braman","first_name":"Virginie S."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"last_name":"Auwerx","full_name":"Auwerx, Johan","first_name":"Johan"},{"full_name":"Hollis, Brian","last_name":"Hollis","first_name":"Brian"},{"first_name":"Bart","last_name":"Deplancke","full_name":"Deplancke, Bart"}],"title":"Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel","abstract":[{"text":"The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.","lang":"eng"}],"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 1","month":"12","publication_status":"published","year":"2019","publication_identifier":{"issn":["2522-5812"]},"language":[{"iso":"eng"}],"publication":"Nature Metabolism","day":"09","page":"1226-1242","date_created":"2020-04-30T10:40:56Z","issue":"12","volume":1,"doi":"10.1038/s42255-019-0147-3","related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-020-0202-0","relation":"erratum"}]},"date_published":"2019-12-09T00:00:00Z"},{"article_processing_charge":"No","author":[{"first_name":"Jonathan","full_name":"Sulc, Jonathan","last_name":"Sulc"},{"first_name":"Ninon","last_name":"Mounier","full_name":"Mounier, Ninon"},{"first_name":"Felix","last_name":"Günther","full_name":"Günther, Felix"},{"first_name":"Thomas","full_name":"Winkler, Thomas","last_name":"Winkler"},{"first_name":"Andrew R.","full_name":"Wood, Andrew R.","last_name":"Wood"},{"last_name":"Frayling","full_name":"Frayling, Timothy M.","first_name":"Timothy M."},{"first_name":"Iris M.","last_name":"Heid","full_name":"Heid, Iris M."},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Zoltán","full_name":"Kutalik, Zoltán","last_name":"Kutalik"}],"title":"Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank","citation":{"chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.","ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .","mla":"Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.","ieee":"J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019).","apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.","ama":"Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019."},"date_updated":"2021-01-12T08:15:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"preprint","status":"public","_id":"7782","page":"20","date_created":"2020-04-30T13:04:26Z","date_published":"2019-06-14T00:00:00Z","year":"2019","publication_status":"published","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"14","main_file_link":[{"url":"https://doi.org/10.1101/632380 ","open_access":"1"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","month":"06","abstract":[{"lang":"eng","text":"As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures."}],"oa_version":"Preprint"},{"_id":"8013","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":["570"],"extern":"1","date_updated":"2021-01-12T08:16:31Z","file_date_updated":"2020-07-14T12:48:08Z","oa_version":"Published Version","pmid":1,"intvolume":" 15","month":"07","language":[{"iso":"eng"}],"file":[{"creator":"cziletti","file_size":773969,"date_updated":"2020-07-14T12:48:08Z","file_name":"2019_PlosCompBio_Currin.pdf","date_created":"2020-07-02T12:22:57Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"723bdfb6ee5c747cbbb32baf01d17fad","file_id":"8079"}],"publication_status":"published","publication_identifier":{"issn":["1553-7358"]},"volume":15,"issue":"7","article_number":"e1007049","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.","apa":"Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049","ama":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049","short":"C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019).","ieee":"C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","chicago":"Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.","ista":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049."},"title":"Think: Theory for Africa","external_id":{"pmid":["31295253"]},"article_processing_charge":"No","author":[{"full_name":"Currin, Christopher B.","last_name":"Currin","first_name":"Christopher B."},{"full_name":"Khoza, Phumlani N.","last_name":"Khoza","first_name":"Phumlani N."},{"first_name":"Alexander D.","last_name":"Antrobus","full_name":"Antrobus, Alexander D."},{"last_name":"Latham","full_name":"Latham, Peter E.","first_name":"Peter E."},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels"},{"full_name":"Raimondo, Joseph V.","last_name":"Raimondo","first_name":"Joseph V."}],"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLOS Computational Biology","day":"11","year":"2019","has_accepted_license":"1","date_created":"2020-06-25T12:50:39Z","date_published":"2019-07-11T00:00:00Z","doi":"10.1371/journal.pcbi.1007049"},{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ama":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017","apa":"Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017","short":"S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12.","ieee":"S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019.","mla":"Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017.","ista":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12.","chicago":"Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017."},"title":"Neural mechanisms of attending to items in working memory","author":[{"full_name":"Manohar, Sanjay G.","last_name":"Manohar","first_name":"Sanjay G."},{"first_name":"Nahid","last_name":"Zokaei","full_name":"Zokaei, Nahid"},{"last_name":"Fallon","full_name":"Fallon, Sean J.","first_name":"Sean J."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels"},{"full_name":"Husain, Masud","last_name":"Husain","first_name":"Masud"}],"article_processing_charge":"No","external_id":{"pmid":["30922977"]},"publisher":"Elsevier ","quality_controlled":"1","oa":1,"day":"01","publication":"Neuroscience and Biobehavioral Reviews","has_accepted_license":"1","year":"2019","doi":"10.1016/j.neubiorev.2019.03.017","date_published":"2019-06-01T00:00:00Z","date_created":"2020-06-25T12:52:13Z","page":"1-12","_id":"8014","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)"},"extern":"1","ddc":["570"],"date_updated":"2021-01-12T08:16:31Z","file_date_updated":"2020-07-14T12:48:08Z","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework."}],"month":"06","intvolume":" 101","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/233007 "}],"file":[{"checksum":"7b972e3d6f7bb3122c8c5648f44e60ca","file_id":"8080","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-02T13:17:52Z","file_name":"2019_NeurosBiobehavRev_Manohar.pdf","creator":"cziletti","date_updated":"2020-07-14T12:48:08Z","file_size":1754418}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0149-7634"]},"publication_status":"published","volume":101},{"date_created":"2020-07-26T22:01:04Z","date_published":"2019-07-01T00:00:00Z","publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","day":"01","year":"2019","oa":1,"quality_controlled":"1","publisher":"Formal Power Series and Algebraic Combinatorics","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","title":"New edge asymptotics of skew Young diagrams via free boundaries","external_id":{"arxiv":["1902.08750"]},"article_processing_charge":"No","author":[{"last_name":"Betea","full_name":"Betea, Dan","first_name":"Dan"},{"first_name":"Jérémie","full_name":"Bouttier, Jérémie","last_name":"Bouttier"},{"full_name":"Nejjar, Peter","last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mirjana","full_name":"Vuletíc, Mirjana","last_name":"Vuletíc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"34","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.08750"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:17:18Z","status":"public","conference":{"name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics","start_date":"2019-07-01","location":"Ljubljana, Slovenia","end_date":"2019-07-05"},"type":"conference","_id":"8175"},{"intvolume":" 12","month":"07","main_file_link":[{"url":"https://doi.org/10.1016/j.waojou.2019.100044","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge.","lang":"eng"}],"issue":"7","volume":12,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1939-4551"]},"status":"public","article_type":"original","type":"journal_article","_id":"8228","extern":"1","date_updated":"2021-01-12T08:17:36Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2020-08-10T11:50:54Z","date_published":"2019-07-29T00:00:00Z","doi":"10.1016/j.waojou.2019.100044","publication":"World Allergy Organization Journal","day":"29","year":"2019","article_number":"100044","title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","article_processing_charge":"No","author":[{"last_name":"Singer","orcid":"0000-0002-8701-2412","full_name":"Singer, Josef","first_name":"Josef"},{"full_name":"Achatz-Straussberger, Gertrude","last_name":"Achatz-Straussberger","first_name":"Gertrude"},{"first_name":"Anna","last_name":"Bentley-Lukschal","full_name":"Bentley-Lukschal, Anna"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Achatz, Gernot","last_name":"Achatz","first_name":"Gernot"},{"last_name":"Karagiannis","full_name":"Karagiannis, Sophia N.","first_name":"Sophia N."},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.","short":"J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).","ieee":"J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.","apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044","ama":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044","chicago":"Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.","ista":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044."}},{"intvolume":" 11","month":"10","main_file_link":[{"url":"https://doi.org/10.3390/nu11102463","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response.","lang":"eng"}],"issue":"10","volume":11,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2072-6643"]},"status":"public","type":"journal_article","article_type":"original","_id":"8229","extern":"1","date_updated":"2021-01-12T08:17:36Z","oa":1,"quality_controlled":"1","publisher":"MDPI","date_created":"2020-08-10T11:51:04Z","date_published":"2019-10-15T00:00:00Z","doi":"10.3390/nu11102463","publication":"Nutrients","day":"15","year":"2019","article_number":"2463","title":"Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model","article_processing_charge":"No","author":[{"first_name":"Anna S.","last_name":"Ondracek","orcid":"0000-0001-7625-3651","full_name":"Ondracek, Anna S."},{"first_name":"Denise","full_name":"Heiden, Denise","last_name":"Heiden"},{"full_name":"Oostingh, Gertie J.","last_name":"Oostingh","first_name":"Gertie J."},{"full_name":"Fuerst, Elisabeth","last_name":"Fuerst","first_name":"Elisabeth"},{"last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit"},{"full_name":"Bergmayr, Cornelia","last_name":"Bergmayr","first_name":"Cornelia"},{"first_name":"Johanna","full_name":"Rohrhofer, Johanna","orcid":"0000-0002-2783-2099","last_name":"Rohrhofer"},{"first_name":"Erika","last_name":"Jensen-Jarolim","orcid":"0000-0003-4019-5765","full_name":"Jensen-Jarolim, Erika"},{"first_name":"Albert","orcid":"0000-0002-7034-9860","full_name":"Duschl, Albert","last_name":"Duschl"},{"first_name":"Eva","last_name":"Untersmayr","orcid":"0000-0002-1963-499X","full_name":"Untersmayr, Eva"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463.","chicago":"Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.","apa":"Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463","ama":"Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463","short":"A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).","ieee":"A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019.","mla":"Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463."}},{"publication":"Allergy","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2019","publication_identifier":{"issn":["0105-4538","1398-9995"]},"date_created":"2020-08-10T11:50:42Z","doi":"10.1111/all.13818","volume":74,"date_published":"2019-10-01T00:00:00Z","issue":"10","page":"1985-1989","oa_version":"Published Version","intvolume":" 74","month":"10","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13818"}],"quality_controlled":"1","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.","apa":"Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818","ama":"Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818","short":"K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.","ieee":"K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.","chicago":"Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.","ista":"Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989."},"date_updated":"2021-01-12T08:17:35Z","title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","article_processing_charge":"No","author":[{"full_name":"Ilieva, Kristina M.","last_name":"Ilieva","first_name":"Kristina M."},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Bax, Heather J.","last_name":"Bax","first_name":"Heather J."},{"last_name":"Crescioli","full_name":"Crescioli, Silvia","first_name":"Silvia"},{"last_name":"Montero‐Morales","full_name":"Montero‐Morales, Laura","first_name":"Laura"},{"last_name":"Mele","full_name":"Mele, Silvia","first_name":"Silvia"},{"first_name":"Heng Sheng","full_name":"Sow, Heng Sheng","last_name":"Sow"},{"full_name":"Stavraka, Chara","last_name":"Stavraka","first_name":"Chara"},{"full_name":"Josephs, Debra H.","last_name":"Josephs","first_name":"Debra H."},{"full_name":"Spicer, James F.","last_name":"Spicer","first_name":"James F."},{"first_name":"Herta","full_name":"Steinkellner, Herta","orcid":"0000-0003-4823-1505","last_name":"Steinkellner"},{"first_name":"Erika","orcid":"0000-0003-4019-5765","full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim"},{"first_name":"Andrew N. J.","last_name":"Tutt","orcid":"0000-0001-8715-2901","full_name":"Tutt, Andrew N. J."},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","orcid":"0000-0002-4100-7810","last_name":"Karagiannis"}],"_id":"8227","status":"public","type":"journal_article","article_type":"letter_note"},{"month":"03","intvolume":" 19","publisher":"Springer Nature","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines."}],"date_published":"2019-03-27T00:00:00Z","doi":"10.1186/s12862-019-1403-6","volume":19,"date_created":"2020-08-15T11:04:07Z","day":"27","publication":"BMC Evolutionary Biology","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1471-2148"]},"publication_status":"published","year":"2019","status":"public","article_type":"original","type":"journal_article","article_number":"83","_id":"8263","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","author":[{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","orcid":"0000-0003-0120-9319","last_name":"Shelyakin"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"first_name":"Anna A.","full_name":"Karan, Anna A.","last_name":"Karan"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:28:54Z","citation":{"ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6","apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6."}},{"abstract":[{"lang":"eng","text":"While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting."}],"oa_version":"None","scopus_import":"1","publisher":"ACM","quality_controlled":"1","month":"05","publication_identifier":{"isbn":["9781450367271"]},"year":"2019","publication_status":"published","day":"01","publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","language":[{"iso":"eng"}],"page":"105-112","doi":"10.1145/3317550.3321448","date_published":"2019-05-01T00:00:00Z","date_created":"2020-08-26T11:45:45Z","_id":"8296","type":"conference","conference":{"start_date":"2019-05-13","end_date":"2019-05-15","location":"Bertinoro, Italy","name":"HotOS: Workshop on Hot Topics in Operating Systems"},"status":"public","citation":{"ista":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.","chicago":"Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.","ieee":"E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112.","short":"E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.","apa":"Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448","ama":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448","mla":"Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448."},"date_updated":"2021-01-12T08:17:56Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Enis Ceyhun","full_name":"Alp, Enis Ceyhun","last_name":"Alp"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Georgia","last_name":"Fragkouli","full_name":"Fragkouli, Georgia"},{"full_name":"Ford, Bryan","last_name":"Ford","first_name":"Bryan"}],"article_processing_charge":"No","title":"Rethinking general-purpose decentralized computing"},{"date_created":"2020-08-26T12:16:38Z","date_published":"2019-10-01T00:00:00Z","year":"2019","publication_status":"submitted","publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1128 "}],"month":"10","abstract":[{"text":"Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","author":[{"first_name":"Alexei","last_name":"Zamyatin","full_name":"Zamyatin, Alexei"},{"first_name":"Mustafa","full_name":"Al-Bassam, Mustafa","last_name":"Al-Bassam"},{"first_name":"Dionysis","full_name":"Zindros, Dionysis","last_name":"Zindros"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"last_name":"Kiayias","full_name":"Kiayias, Aggelos","first_name":"Aggelos"},{"last_name":"Knottenbelt","full_name":"Knottenbelt, William J.","first_name":"William J."}],"title":"SoK: Communication across distributed ledgers","date_updated":"2021-09-24T12:08:14Z","citation":{"ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","type":"preprint","status":"public","_id":"8304","article_number":"2019/1128"},{"citation":{"chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d.","ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676.","mla":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676.","ama":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","apa":"Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","ieee":"E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. .","short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.)."},"date_updated":"2021-09-24T12:07:11Z","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"}],"article_processing_charge":"No","title":"Robust and scalable consensus for sharded distributed ledgers","_id":"8303","article_number":"2019/676","type":"preprint","status":"public","year":"2019","publication_status":"submitted","day":"06","publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"date_published":"2019-06-06T00:00:00Z","date_created":"2020-08-26T12:13:56Z","abstract":[{"lang":"eng","text":"ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/676"}],"oa":1,"month":"06"},{"status":"public","type":"dissertation","_id":"8311","title":"Secure, confidential blockchains providing high throughput and low latency","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"}],"article_processing_charge":"No","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"last_name":"Ford","full_name":"Ford, Bryan Alexander","first_name":"Bryan Alexander"}],"citation":{"ama":"Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101","apa":"Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101","short":"E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.","ieee":"E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019.","mla":"Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101.","ista":"Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne.","chicago":"Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101."},"date_updated":"2021-12-20T15:30:47Z","month":"09","publisher":"École Polytechnique Fédérale de Lausanne","main_file_link":[{"url":"https://www.doi.org/10.5075/epfl-thesis-7101","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope."}],"date_published":"2019-09-27T00:00:00Z","doi":"10.5075/epfl-thesis-7101","date_created":"2020-08-27T11:22:24Z","page":"244","day":"27","language":[{"iso":"eng"}],"degree_awarded":"PhD","year":"2019","publication_status":"published"},{"title":"Brick: Asynchronous payment channels","author":[{"first_name":"Georgia","last_name":"Avarikioti","full_name":"Avarikioti, Georgia"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Wattenhofer","full_name":"Wattenhofer, Roger","first_name":"Roger"},{"last_name":"Zindros","full_name":"Zindros, Dionysis","first_name":"Dionysis"}],"external_id":{"arxiv":["1905.11360"]},"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.","ieee":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” arXiv. .","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv.","apa":"Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.). Brick: Asynchronous payment channels. arXiv.","mla":"Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv, 1905.11360."},"date_updated":"2021-01-12T08:18:04Z","status":"public","type":"preprint","article_number":"1905.11360","_id":"8314","date_published":"2019-05-27T00:00:00Z","date_created":"2020-08-27T11:36:54Z","day":"27","publication":"arXiv","language":[{"iso":"eng"}],"year":"2019","publication_status":"submitted","month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"oa_version":"Preprint","abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called Wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee's approval for the last valid state. Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. Furthermore, we consider permissioned blockchains, where the additional property of auditability might be desired for regulatory purposes. We introduce Brick+, an off-chain construction that provides auditability on top of Brick without conflicting with its privacy guarantees. We formally define the properties our payment channel construction should fulfill, and prove that both Brick and Brick+ satisfy them. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}]},{"_id":"8315","article_number":"1910.10434","type":"preprint","status":"public","citation":{"ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, n.d.","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.).","ieee":"G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” arXiv. .","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","apa":"Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","mla":"Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, 1910.10434."},"date_updated":"2021-01-12T08:18:05Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Georgia","last_name":"Avarikioti","full_name":"Avarikioti, Georgia"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Roger","full_name":"Wattenhofer, Roger","last_name":"Wattenhofer"}],"external_id":{"arxiv":["1910.10434"]},"article_processing_charge":"No","title":"Divide and scale: Formalization of distributed ledger sharding protocols","abstract":[{"text":"Sharding distributed ledgers is the most promising on-chain solution for scaling blockchain technology. In this work, we define and analyze the properties a sharded distributed ledger should fulfill. More specifically, we show that a sharded blockchain cannot be scalable under a fully adaptive adversary, but it can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible only if the distributed ledger creates succinct proofs of the valid state updates at the end of each epoch. Our model builds upon and extends the Bitcoin backbone protocol by defining consistency and\r\nscalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system. In\r\norder to show the power of our framework, we analyze the most prominent sharded blockchains and either prove their correctness (OmniLedger, RapidChain) under our model or pinpoint where they fail to balance the consistency and\r\nscalability requirements (Elastico, Monoxide). ","lang":"eng"}],"oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10434"}],"month":"10","year":"2019","publication_status":"submitted","day":"23","language":[{"iso":"eng"}],"publication":"arXiv","date_published":"2019-10-23T00:00:00Z","date_created":"2020-08-27T11:37:43Z"},{"day":"22","year":"2019","ipc":"G06F21/62 ; H04L9/08 ; H04L9/32","date_published":"2019-08-22T00:00:00Z","date_created":"2020-08-27T11:24:44Z","publication_date":"2019-08-22","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The present invention concerns a computer-implemented method for secure data exchange between a sender (A) and a recipient (B), wherein the method is performed by the sender (A) and comprises encrypting data using a symmetric key k, creating a write transaction T W , wherein the write transaction T W comprises information usable to derive the symmetric key k and an access policy identifying the recipient (B) as being allowed to decrypt the encrypted data, providing the recipient (B) access to the encrypted data, and sending the write transaction T W to a first group of servers (AC) for being stored in a blockchain data structure maintained by the first group of servers (AC)."}],"month":"08","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/WO2019158209A1"}],"oa":1,"extern":"1","ipn":"WO2019158209 (A1)","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-05T14:00:32Z","citation":{"ista":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for secure data exchange.","chicago":"Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “Methods and Systems for Secure Data Exchange,” 2019.","ama":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019.","apa":"Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods and systems for secure data exchange.","ieee":"B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019.","short":"B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).","mla":"Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019."},"title":"Methods and systems for secure data exchange","author":[{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"},{"first_name":"Linus","last_name":"Gasser","full_name":"Gasser, Linus"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Janovic, Philipp","last_name":"Janovic","first_name":"Philipp"}],"article_processing_charge":"No","applicant":["École Polytechnique Fédérale De Lausanne "],"_id":"8313","status":"public","type":"patent"},{"article_processing_charge":"No","external_id":{"pmid":["31217444"]},"author":[{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"first_name":"Leandro F.","last_name":"Estrozi","full_name":"Estrozi, Leandro F."},{"last_name":"Schwieters","full_name":"Schwieters, Charles D.","first_name":"Charles D."},{"full_name":"Effantin, Gregory","last_name":"Effantin","first_name":"Gregory"},{"first_name":"Pavel","full_name":"Macek, Pavel","last_name":"Macek"},{"last_name":"Sounier","full_name":"Sounier, Remy","first_name":"Remy"},{"last_name":"Sivertsen","full_name":"Sivertsen, Astrid C.","first_name":"Astrid C."},{"first_name":"Elena","full_name":"Schmidt, Elena","last_name":"Schmidt"},{"last_name":"Kerfah","full_name":"Kerfah, Rime","first_name":"Rime"},{"first_name":"Guillaume","full_name":"Mas, Guillaume","last_name":"Mas"},{"first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe","last_name":"Colletier"},{"first_name":"Peter","full_name":"Güntert, Peter","last_name":"Güntert"},{"first_name":"Adrien","last_name":"Favier","full_name":"Favier, Adrien"},{"last_name":"Schoehn","full_name":"Schoehn, Guy","first_name":"Guy"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Jerome","last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome"}],"title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","citation":{"chicago":"Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.","ista":"Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697.","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.","ieee":"D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019.","short":"D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).","ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9","apa":"Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2697","date_created":"2020-09-17T10:28:25Z","doi":"10.1038/s41467-019-10490-9","date_published":"2019-06-19T00:00:00Z","year":"2019","publication":"Nature Communications","day":"19","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2021-01-12T08:19:03Z","extern":"1","type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","_id":"8405","volume":10,"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41467-019-10490-9","open_access":"1"}],"intvolume":" 10","month":"06","abstract":[{"text":"Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation."}],"oa_version":"Published Version","main_file_link":[{"url":" https://doi.org/10.1126/sciadv.aaw3818","open_access":"1"}],"month":"09","intvolume":" 5","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":5,"issue":"9","_id":"8406","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T08:19:03Z","extern":"1","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"year":"2019","day":"04","publication":"Science Advances","date_published":"2019-09-04T00:00:00Z","doi":"10.1126/sciadv.aaw3818","date_created":"2020-09-17T10:28:36Z","article_number":"eaaw3818","citation":{"short":"J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019).","ieee":"J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","apa":"Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818","ama":"Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818","mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818.","ista":"Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818.","chicago":"Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Felix, Jan","last_name":"Felix","first_name":"Jan"},{"full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl","first_name":"Katharina"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Morlot","full_name":"Morlot, Cecile","first_name":"Cecile"},{"last_name":"Abian","full_name":"Abian, Olga","first_name":"Olga"},{"last_name":"Gutsche","full_name":"Gutsche, Irina","first_name":"Irina"},{"full_name":"Velazquez-Campoy, Adrian","last_name":"Velazquez-Campoy","first_name":"Adrian"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"}],"article_processing_charge":"No","title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors"},{"publisher":"American Chemical Society","quality_controlled":"1","date_created":"2020-09-17T10:29:50Z","doi":"10.1021/jacs.8b09258","date_published":"2019-01-08T00:00:00Z","page":"858-869","publication":"Journal of the American Chemical Society","day":"08","year":"2019","title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","external_id":{"pmid":["30620186"]},"article_processing_charge":"No","author":[{"first_name":"Petra","last_name":"Rovó","full_name":"Rovó, Petra"},{"full_name":"Smith, Colin A.","last_name":"Smith","first_name":"Colin A."},{"first_name":"Diego","last_name":"Gauto","full_name":"Gauto, Diego"},{"last_name":"de Groot","full_name":"de Groot, Bert L.","first_name":"Bert L."},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Rasmus","last_name":"Linser","full_name":"Linser, Rasmus"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258","apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869.","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019.","mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.","ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869.","chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258."},"intvolume":" 141","month":"01","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.","lang":"eng"}],"issue":"2","volume":141,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0002-7863","1520-5126"]},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"original","_id":"8413","extern":"1","date_updated":"2021-01-12T08:19:07Z"},{"publication_identifier":{"issn":["1439-4235"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":20,"issue":"2","abstract":[{"lang":"eng","text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid."}],"pmid":1,"oa_version":"Submitted Version","month":"01","intvolume":" 20","date_updated":"2021-01-12T08:19:06Z","extern":"1","_id":"8412","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"year":"2019","day":"21","publication":"ChemPhysChem","page":"311-317","date_published":"2019-01-21T00:00:00Z","doi":"10.1002/cphc.201800779","date_created":"2020-09-17T10:29:43Z","quality_controlled":"1","publisher":"Wiley","citation":{"ieee":"M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779","apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779","mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.","ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.","chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matthew D.","last_name":"Shannon","full_name":"Shannon, Matthew D."},{"first_name":"Theint","full_name":"Theint, Theint","last_name":"Theint"},{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Dwaipayan","first_name":"Dwaipayan"},{"full_name":"Surewicz, Krystyna","last_name":"Surewicz","first_name":"Krystyna"},{"full_name":"Surewicz, Witold K.","last_name":"Surewicz","first_name":"Witold K."},{"last_name":"Marion","full_name":"Marion, Dominique","first_name":"Dominique"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"last_name":"Jaroniec","full_name":"Jaroniec, Christopher P.","first_name":"Christopher P."}],"article_processing_charge":"No","external_id":{"pmid":["30276945"]},"title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR"},{"date_updated":"2021-01-12T08:19:06Z","extern":"1","_id":"8411","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"publication_identifier":{"issn":["1439-4235"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":20,"abstract":[{"lang":"eng","text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin."}],"pmid":1,"oa_version":"Submitted Version","month":"01","intvolume":" 20","citation":{"short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284.","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935","apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935","mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.","ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284.","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Marion, Dominique","last_name":"Marion","first_name":"Dominique"},{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"first_name":"Karine","last_name":"Giandoreggio-Barranco","full_name":"Giandoreggio-Barranco, Karine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"article_processing_charge":"No","external_id":{"pmid":["30444575"]},"title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","year":"2019","day":"21","publication":"ChemPhysChem","page":"276-284","date_published":"2019-01-21T00:00:00Z","doi":"10.1002/cphc.201800935","date_created":"2020-09-17T10:29:36Z","quality_controlled":"1","publisher":"Wiley"},{"publication":"Communications in Mathematical Physics","day":"09","year":"2019","date_created":"2020-09-17T10:41:27Z","date_published":"2019-05-09T00:00:00Z","doi":"10.1007/s00220-019-03448-x","page":"1531-1575","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x","apa":"Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575.","chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x."},"title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","article_processing_charge":"No","external_id":{"arxiv":["1809.08947"]},"author":[{"first_name":"Péter","last_name":"Bálint","full_name":"Bálint, Péter"},{"last_name":"De Simoi","full_name":"De Simoi, Jacopo","first_name":"Jacopo"},{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"},{"first_name":"Martin","last_name":"Leguil","full_name":"Leguil, Martin"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-3616","1432-0916"]},"volume":374,"issue":"3","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit."}],"intvolume":" 374","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08947"}],"extern":"1","date_updated":"2021-01-12T08:19:08Z","_id":"8415","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"status":"public","article_type":"original","type":"journal_article"},{"title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","article_processing_charge":"No","external_id":{"pmid":["30031884"]},"author":[{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"last_name":"Ayala","full_name":"Ayala, Isabel","first_name":"Isabel"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"},{"last_name":"Simorre","full_name":"Simorre, Jean-Pierre","first_name":"Jean-Pierre"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.","ista":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72.","mla":"Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.","apa":"Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009","ama":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009","short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","ieee":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019."},"date_created":"2020-09-17T10:29:10Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1016/j.jsb.2018.07.009","page":"66-72","publication":"Journal of Structural Biology","day":"01","year":"2019","quality_controlled":"1","publisher":"Elsevier","extern":"1","date_updated":"2021-01-12T08:19:05Z","keyword":["Structural Biology"],"status":"public","type":"journal_article","article_type":"original","_id":"8409","volume":206,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1047-8477"]},"intvolume":" 206","month":"04","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling."}]},{"oa_version":"Submitted Version","pmid":1,"publisher":"Elsevier","quality_controlled":"1","month":"09","intvolume":" 306","publication_identifier":{"issn":["1090-7807"]},"year":"2019","publication_status":"published","day":"01","publication":"Journal of Magnetic Resonance","language":[{"iso":"eng"}],"page":"180-186","volume":306,"date_published":"2019-09-01T00:00:00Z","doi":"10.1016/j.jmr.2019.07.025","date_created":"2020-09-17T10:28:47Z","_id":"8407","type":"journal_article","article_type":"original","status":"public","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"date_updated":"2021-01-12T08:19:04Z","citation":{"ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186.","chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.","short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019.","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025","apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"external_id":{"pmid":["31350165"]},"article_processing_charge":"No","title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics"},{"main_file_link":[{"url":"https://doi.org/10.1002/cphc.201801100","open_access":"1"}],"intvolume":" 20","month":"01","oa_version":"Published Version","pmid":1,"issue":"2","volume":20,"publication_status":"published","publication_identifier":{"issn":["1439-4235"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"letter_note","status":"public","_id":"8410","date_updated":"2021-01-12T08:19:05Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"Wiley","page":"177-177","date_created":"2020-09-17T10:29:26Z","date_published":"2019-01-21T00:00:00Z","doi":"10.1002/cphc.201801100","year":"2019","publication":"ChemPhysChem","day":"21","external_id":{"pmid":["30556633"]},"article_processing_charge":"No","author":[{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"last_name":"Chekmenev","full_name":"Chekmenev, Eduard Y.","first_name":"Eduard Y."}],"title":"NMR for Biological Systems","citation":{"chicago":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201801100.","ista":"Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177.","mla":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100.","ieee":"P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 177–177, 2019.","short":"P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.","ama":"Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177. doi:10.1002/cphc.201801100","apa":"Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201801100"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"quality_controlled":"1","publisher":"EasyChair","intvolume":" 61","month":"05","abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.","lang":"eng"}],"oa_version":"Published Version","page":"14-40","date_created":"2020-09-26T14:23:54Z","doi":"10.29007/bj1w","date_published":"2019-05-25T00:00:00Z","volume":61,"year":"2019","publication_status":"published","publication_identifier":{"eissn":["23987340"]},"publication":"EPiC Series in Computing","language":[{"iso":"eng"}],"day":"25","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","location":"Montreal, Canada","end_date":"2019-04-15","start_date":"2019-04-15"},"type":"conference","status":"public","_id":"8570","article_processing_charge":"No","author":[{"first_name":"Matthias","last_name":"Althoff","full_name":"Althoff, Matthias"},{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"last_name":"Ray","full_name":"Ray, Rajarshi","first_name":"Rajarshi"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Schupp, Stefan","last_name":"Schupp","first_name":"Stefan"}],"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","department":[{"_id":"ToHe"}],"citation":{"mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.","ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40."},"date_updated":"2021-01-12T08:20:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","author":[{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","last_name":"Bakail"},{"first_name":"Silvia","full_name":"Rodriguez‐Marin, Silvia","last_name":"Rodriguez‐Marin"},{"first_name":"Zsófia","last_name":"Hegedüs","full_name":"Hegedüs, Zsófia"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"},{"full_name":"Wilson, Andrew J.","last_name":"Wilson","first_name":"Andrew J."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633."},"publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2019-04-01T00:00:00Z","doi":"10.1002/cbic.201800633","date_created":"2021-01-19T10:59:14Z","page":"891-895","day":"01","publication":"ChemBioChem","year":"2019","status":"public","type":"journal_article","article_type":"original","_id":"9016","extern":"1","date_updated":"2023-02-23T13:46:48Z","month":"04","intvolume":" 20","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1002/cbic.201800633"}],"oa_version":"Published Version","abstract":[{"text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs.","lang":"eng"}],"issue":"7","volume":20,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1439-4227","1439-7633"]},"publication_status":"published"},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.","lang":"eng"}],"month":"07","intvolume":" 10","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"70c6e5d6fbea0932b0669505ab6633ec","file_id":"9061","creator":"cziletti","file_size":2820337,"date_updated":"2021-02-02T13:47:21Z","file_name":"2019_NatureComm_Ramananarivo.pdf","date_created":"2021-02-02T13:47:21Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","volume":10,"issue":"1","_id":"9060","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"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)"},"extern":"1","ddc":["530"],"date_updated":"2023-02-23T13:47:59Z","file_date_updated":"2021-02-02T13:47:21Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"29","publication":"Nature Communications","has_accepted_license":"1","year":"2019","doi":"10.1038/s41467-019-11362-y","date_published":"2019-07-29T00:00:00Z","date_created":"2021-02-02T13:43:36Z","article_number":"3380","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.","apa":"Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y.","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380."},"title":"Activity-controlled annealing of colloidal monolayers","author":[{"last_name":"Ramananarivo","full_name":"Ramananarivo, Sophie","first_name":"Sophie"},{"full_name":"Ducrot, Etienne","last_name":"Ducrot","first_name":"Etienne"},{"last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"external_id":{"arxiv":["1909.07382"],"pmid":["31358762"]},"article_processing_charge":"No"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"19","volume":116,"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","file_id":"9461","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_PNAS_Kim.pdf","date_created":"2021-06-04T12:50:47Z","file_size":1142540,"date_updated":"2021-06-04T12:50:47Z","creator":"asandaue"}],"scopus_import":"1","intvolume":" 116","month":"05","abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-04T12:50:47Z","date_updated":"2021-12-14T07:52:30Z","ddc":["580"],"extern":"1","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","keyword":["Multidisciplinary"],"status":"public","_id":"9460","page":"9652-9657","date_created":"2021-06-04T12:38:20Z","doi":"10.1073/pnas.1821435116","date_published":"2019-05-07T00:00:00Z","year":"2019","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"07","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","external_id":{"pmid":["31000601"]},"article_processing_charge":"No","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"last_name":"Ono","full_name":"Ono, Akemi","first_name":"Akemi"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"},{"first_name":"Tetsu","full_name":"Kinoshita, Tetsu","last_name":"Kinoshita"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","citation":{"ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"page":"1110-1115","doi":"10.1073/pnas.1815117116","date_published":"2019-01-22T00:00:00Z","date_created":"2021-07-19T10:17:09Z","year":"2019","day":"22","publication":"Proceedings of the National Academy of Sciences","author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Engel","full_name":"Engel, Edgar A.","first_name":"Edgar A."},{"first_name":"Jörg","last_name":"Behler","full_name":"Behler, Jörg"},{"first_name":"Christoph","last_name":"Dellago","full_name":"Dellago, Christoph"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"article_processing_charge":"No","external_id":{"arxiv":["1811.08630"],"pmid":["30610171"]},"title":"Ab initio thermodynamics of liquid and solid water","citation":{"mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 2019;116(4):1110-1115. doi:10.1073/pnas.1815117116","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” Proceedings of the National Academy of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1815117116"}],"month":"01","intvolume":" 116","abstract":[{"text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":116,"issue":"4","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9689","date_updated":"2023-02-23T14:05:08Z","extern":"1"},{"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":"6819","department":[{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:47:40Z","ddc":["570"],"date_updated":"2023-02-23T14:08:14Z","month":"08","intvolume":" 12","scopus_import":1,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"9784","relation":"research_data"}]},"volume":12,"file":[{"date_updated":"2020-07-14T12:47:40Z","file_size":1177482,"creator":"dernst","date_created":"2019-08-23T11:10:35Z","file_name":"2019_BMC_Antoniou.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6829","checksum":"4a2bb7994b7f2c432bf44f5127ea3102"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1756-0500"]},"publication_status":"published","article_number":"494","title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","author":[{"first_name":"Michael N.","full_name":"Antoniou, Michael N.","last_name":"Antoniou"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"first_name":"Robin","last_name":"Mesnage","full_name":"Mesnage, Robin"},{"last_name":"Biserni","full_name":"Biserni, Martina","first_name":"Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"external_id":{"pmid":["31395095"]},"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494."},"quality_controlled":"1","publisher":"BioMed Central","oa":1,"doi":"10.1186/s13104-019-4534-3","date_published":"2019-08-08T00:00:00Z","date_created":"2019-08-18T22:00:39Z","day":"08","publication":"BMC Research Notes","has_accepted_license":"1","year":"2019"},{"oa_version":"Published Version","abstract":[{"text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.","lang":"eng"}],"month":"08","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"publisher":"Springer Nature","day":"09","year":"2019","date_created":"2021-08-06T08:14:05Z","doi":"10.6084/m9.figshare.9411761.v1","related_material":{"record":[{"status":"public","id":"6819","relation":"used_in_publication"}]},"date_published":"2019-08-09T00:00:00Z","_id":"9784","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1."},"date_updated":"2023-02-23T12:52:29Z","department":[{"_id":"LifeSc"}],"title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","article_processing_charge":"No","author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"first_name":"Robin","last_name":"Mesnage","full_name":"Mesnage, Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","last_name":"Martin","first_name":"Cristina Vazquez"}]},{"abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.5vv37","open_access":"1"}],"month":"06","year":"2019","day":"22","date_published":"2019-06-22T00:00:00Z","related_material":{"record":[{"id":"315","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.5vv37","date_created":"2021-08-09T13:07:28Z","_id":"9839","type":"research_data_reference","status":"public","citation":{"mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","short":"J. Polechova, (2019).","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37."},"date_updated":"2023-02-23T11:14:30Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Data from: Is the sky the limit? On the expansion threshold of a species' range"},{"publisher":"American Chemical Society","quality_controlled":"1","date_published":"2019-06-14T00:00:00Z","doi":"10.1021/jacs.9b04219","date_created":"2020-09-17T10:29:00Z","page":"11183-11195","day":"14","publication":"Journal of the American Chemical Society","year":"2019","title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"first_name":"Alessandro","full_name":"Barducci, Alessandro","last_name":"Barducci"},{"first_name":"Hugo","full_name":"Fraga, Hugo","last_name":"Fraga"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"first_name":"Tsutomu","full_name":"Terauchi, Tsutomu","last_name":"Terauchi"},{"first_name":"David","last_name":"Gajan","full_name":"Gajan, David"},{"full_name":"Miyanoiri, Yohei","last_name":"Miyanoiri","first_name":"Yohei"},{"first_name":"Jerome","full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"last_name":"Kainosho","full_name":"Kainosho, Masatsune","first_name":"Masatsune"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}],"article_processing_charge":"No","external_id":{"pmid":["31199882"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","ieee":"D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” Journal of the American Chemical Society, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 2019;141(28):11183-11195. doi:10.1021/jacs.9b04219","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b04219","mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219.","ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219."},"month":"06","intvolume":" 141","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.","lang":"eng"}],"volume":141,"issue":"28","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"type":"journal_article","article_type":"original","_id":"8408","extern":"1","date_updated":"2021-01-12T08:19:04Z"},{"date_updated":"2021-01-12T08:19:09Z","extern":"1","_id":"8418","type":"journal_article","article_type":"original","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0003-9527","1432-0673"]},"language":[{"iso":"eng"}],"volume":233,"issue":"2","abstract":[{"lang":"eng","text":"For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00205-019-01368-7"}],"intvolume":" 233","month":"03","citation":{"mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7","apa":"Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836.","chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7.","ista":"Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Marcel","full_name":"Guardia, Marcel","last_name":"Guardia"},{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Zhang","full_name":"Zhang, Jianlu","first_name":"Jianlu"}],"title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem","year":"2019","publication":"Archive for Rational Mechanics and Analysis","day":"12","page":"799-836","date_created":"2020-09-17T10:41:51Z","doi":"10.1007/s00205-019-01368-7","date_published":"2019-03-12T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"publication_identifier":{"issn":["1609-4514"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":19,"issue":"2","abstract":[{"text":"In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.09341","open_access":"1"}],"month":"04","intvolume":" 19","date_updated":"2021-01-12T08:19:08Z","extern":"1","_id":"8416","type":"journal_article","article_type":"original","status":"public","year":"2019","day":"01","publication":"Moscow Mathematical Journal","page":"307-327","doi":"10.17323/1609-4514-2019-19-2-307-327","date_published":"2019-04-01T00:00:00Z","date_created":"2020-09-17T10:41:36Z","publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"citation":{"mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:10.17323/1609-4514-2019-19-2-307-327.","ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” Moscow Mathematical Journal, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.","apa":"Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327","chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.","ista":"Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Guan","last_name":"Huang","full_name":"Huang, Guan"},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"}],"article_processing_charge":"No","external_id":{"arxiv":["1809.09341"]},"title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables"},{"oa_version":"Preprint","abstract":[{"text":"We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed.","lang":"eng"}],"intvolume":" 24","month":"12","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.02523","open_access":"1"}],"quality_controlled":"1","publisher":"Springer","language":[{"iso":"eng"}],"publication":"Regular and Chaotic Dynamics","day":"10","year":"2019","publication_status":"published","date_created":"2020-10-21T15:25:45Z","volume":24,"doi":"10.1134/S1560354719060017","date_published":"2019-12-10T00:00:00Z","page":"583–606","_id":"8693","status":"public","type":"journal_article","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"apa":"Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017","ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017","short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.","ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606.","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017."},"date_updated":"2021-01-12T08:20:34Z","title":"V. I. Arnold’s “pointwise” KAM theorem","article_processing_charge":"No","external_id":{"arxiv":["1908.02523"]},"author":[{"first_name":"Luigi","full_name":"Chierchia, Luigi","last_name":"Chierchia"},{"first_name":"Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","last_name":"Koudjinan","full_name":"Koudjinan, Edmond","orcid":"0000-0003-2640-4049"}]},{"citation":{"ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M"},{"last_name":"Gaubert","full_name":"Gaubert, Albane","first_name":"Albane"},{"full_name":"Andreani, Jessica","last_name":"Andreani","first_name":"Jessica"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"first_name":"Guillaume","full_name":"Pinna, Guillaume","last_name":"Pinna"},{"first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina","last_name":"Boyarchuk"},{"first_name":"Marie-Cécile","full_name":"Gaillard, Marie-Cécile","last_name":"Gaillard"},{"last_name":"Courbeyrette","full_name":"Courbeyrette, Regis","first_name":"Regis"},{"first_name":"Carl","full_name":"Mann, Carl","last_name":"Mann"},{"last_name":"Thuret","full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves"},{"last_name":"Guichard","full_name":"Guichard, Bérengère","first_name":"Bérengère"},{"first_name":"Brice","last_name":"Murciano","full_name":"Murciano, Brice"},{"full_name":"Richet, Nicolas","last_name":"Richet","first_name":"Nicolas"},{"first_name":"Adeline","last_name":"Poitou","full_name":"Poitou, Adeline"},{"full_name":"Frederic, Claire","last_name":"Frederic","first_name":"Claire"},{"full_name":"Le Du, Marie-Hélène","last_name":"Le Du","first_name":"Marie-Hélène"},{"last_name":"Agez","full_name":"Agez, Morgane","first_name":"Morgane"},{"last_name":"Roelants","full_name":"Roelants, Caroline","first_name":"Caroline"},{"first_name":"Zachary A.","full_name":"Gurard-Levin, Zachary A.","last_name":"Gurard-Levin"},{"full_name":"Almouzni, Geneviève","last_name":"Almouzni","first_name":"Geneviève"},{"first_name":"Nadia","full_name":"Cherradi, Nadia","last_name":"Cherradi"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"article_processing_charge":"No","external_id":{"pmid":["31543461"]},"title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","year":"2019","day":"21","publication":"Cell Chemical Biology","page":"1573-1585.e10","doi":"10.1016/j.chembiol.2019.09.002","date_published":"2019-11-21T00:00:00Z","date_created":"2021-01-19T11:04:50Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-02-23T13:46:53Z","extern":"1","_id":"9018","type":"journal_article","article_type":"original","status":"public","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"publication_identifier":{"issn":["2451-9456"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"11","volume":26,"abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chembiol.2019.09.002"}],"month":"11","intvolume":" 26"},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"intvolume":" 12","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"86ff50a7517891511af2733c76c81b67","file_id":"9531","file_size":3221067,"date_updated":"2021-06-08T09:29:19Z","creator":"asandaue","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","date_created":"2021-06-08T09:29:19Z"}],"publication_status":"published","publication_identifier":{"eissn":["1756-8935"]},"volume":12,"_id":"9530","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","ddc":["570"],"extern":"1","date_updated":"2021-12-14T07:53:00Z","file_date_updated":"2021-06-08T09:29:19Z","department":[{"_id":"DaZi"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Epigenetics and Chromatin","day":"10","year":"2019","has_accepted_license":"1","date_created":"2021-06-08T09:21:51Z","doi":"10.1186/s13072-019-0307-4","date_published":"2019-10-10T00:00:00Z","article_number":"62","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4."},"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","article_processing_charge":"No","external_id":{"pmid":["31601251"]},"author":[{"first_name":"Keith D.","full_name":"Harris, Keith D.","last_name":"Harris"},{"first_name":"James P. B.","last_name":"Lloyd","full_name":"Lloyd, James P. B."},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"}]},{"extern":"1","date_updated":"2023-02-23T14:01:53Z","_id":"9586","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"issue":"3","volume":99,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Consider integers 𝑘,ℓ such that 0⩽ℓ⩽(𝑘2) . Given a large graph 𝐺 , what is the fraction of 𝑘 -vertex subsets of 𝐺 which span exactly ℓ edges? When 𝐺 is empty or complete, and ℓ is zero or (𝑘2) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any 𝑘 and ℓ , the fraction of 𝑘 -vertex subsets that span ℓ edges is at most log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube."}],"intvolume":" 99","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05202"}],"scopus_import":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192.","apa":"Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777.","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192.","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777."},"title":"Anticoncentration for subgraph statistics","article_processing_charge":"No","external_id":{"arxiv":["1807.05202"]},"author":[{"last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"full_name":"Tran, Tuan","last_name":"Tran","first_name":"Tuan"}],"publication":"Journal of the London Mathematical Society","day":"03","year":"2019","date_created":"2021-06-22T09:46:03Z","date_published":"2019-05-03T00:00:00Z","doi":"10.1112/jlms.12192","page":"757-777","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"intvolume":" 233","month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08462"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation.","lang":"eng"}],"issue":"1","volume":233,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]},"status":"public","type":"journal_article","article_type":"original","_id":"9580","extern":"1","date_updated":"2023-02-23T14:01:41Z","oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2021-06-21T13:36:02Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1007/s11856-019-1897-z","page":"67-111","publication":"Israel Journal of Mathematics","day":"01","year":"2019","title":"Hypergraph cuts above the average","external_id":{"arxiv":["1803.08462"]},"article_processing_charge":"No","author":[{"full_name":"Conlon, David","last_name":"Conlon","first_name":"David"},{"last_name":"Fox","full_name":"Fox, Jacob","first_name":"Jacob"},{"first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111.","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z.","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019.","apa":"Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z","mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z."}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1090/tran/7729"}],"scopus_import":"1","intvolume":" 372","month":"10","abstract":[{"text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture.","lang":"eng"}],"oa_version":"Submitted Version","issue":"8","volume":372,"publication_status":"published","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"9585","date_updated":"2023-02-23T14:01:50Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","page":"5571-5594","date_created":"2021-06-22T09:31:45Z","date_published":"2019-10-15T00:00:00Z","doi":"10.1090/tran/7729","year":"2019","publication":"Transactions of the American Mathematical Society","day":"15","article_processing_charge":"No","external_id":{"arxiv":["1712.05656"]},"author":[{"first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"}],"title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","citation":{"ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.","chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","apa":"Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"title":"i-PI 2.0: A universal force engine for advanced molecular simulations","article_processing_charge":"No","external_id":{"arxiv":["1808.03824"]},"author":[{"first_name":"Venkat","full_name":"Kapil, Venkat","last_name":"Kapil"},{"first_name":"Mariana","full_name":"Rossi, Mariana","last_name":"Rossi"},{"first_name":"Ondrej","last_name":"Marsalek","full_name":"Marsalek, Ondrej"},{"full_name":"Petraglia, Riccardo","last_name":"Petraglia","first_name":"Riccardo"},{"last_name":"Litman","full_name":"Litman, Yair","first_name":"Yair"},{"first_name":"Thomas","last_name":"Spura","full_name":"Spura, Thomas"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng"},{"full_name":"Cuzzocrea, Alice","last_name":"Cuzzocrea","first_name":"Alice"},{"first_name":"Robert H.","full_name":"Meißner, Robert H.","last_name":"Meißner"},{"last_name":"Wilkins","full_name":"Wilkins, David M.","first_name":"David M."},{"first_name":"Benjamin A.","last_name":"Helfrecht","full_name":"Helfrecht, Benjamin A."},{"first_name":"Przemysław","last_name":"Juda","full_name":"Juda, Przemysław"},{"full_name":"Bienvenue, Sébastien P.","last_name":"Bienvenue","first_name":"Sébastien P."},{"last_name":"Fang","full_name":"Fang, Wei","first_name":"Wei"},{"first_name":"Jan","last_name":"Kessler","full_name":"Kessler, Jan"},{"first_name":"Igor","full_name":"Poltavsky, Igor","last_name":"Poltavsky"},{"first_name":"Steven","last_name":"Vandenbrande","full_name":"Vandenbrande, Steven"},{"first_name":"Jelle","full_name":"Wieme, Jelle","last_name":"Wieme"},{"full_name":"Corminboeuf, Clemence","last_name":"Corminboeuf","first_name":"Clemence"},{"full_name":"Kühne, Thomas D.","last_name":"Kühne","first_name":"Thomas D."},{"full_name":"Manolopoulos, David E.","last_name":"Manolopoulos","first_name":"David E."},{"first_name":"Thomas E.","last_name":"Markland","full_name":"Markland, Thomas E."},{"full_name":"Richardson, Jeremy O.","last_name":"Richardson","first_name":"Jeremy O."},{"last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre","first_name":"Alexandre"},{"last_name":"Tribello","full_name":"Tribello, Gareth A.","first_name":"Gareth A."},{"full_name":"Van Speybroeck, Veronique","last_name":"Van Speybroeck","first_name":"Veronique"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223.","chicago":"Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier, 2019. https://doi.org/10.1016/j.cpc.2018.09.020.","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 2019;236:214-223. doi:10.1016/j.cpc.2018.09.020","apa":"Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020","ieee":"V. Kapil et al., “i-PI 2.0: A universal force engine for advanced molecular simulations,” Computer Physics Communications, vol. 236. Elsevier, pp. 214–223, 2019.","short":"V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223.","mla":"Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019, pp. 214–23, doi:10.1016/j.cpc.2018.09.020."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2021-07-16T08:53:01Z","doi":"10.1016/j.cpc.2018.09.020","date_published":"2019-03-01T00:00:00Z","page":"214-223","publication":"Computer Physics Communications","day":"01","year":"2019","status":"public","article_type":"original","type":"journal_article","_id":"9677","extern":"1","date_updated":"2021-08-09T12:37:16Z","intvolume":" 236","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1808.03824","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.","lang":"eng"}],"volume":236,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-4655"]}},{"author":[{"last_name":"Giberti","full_name":"Giberti, F.","first_name":"F."},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"last_name":"Tribello","full_name":"Tribello, G. A.","first_name":"G. A."},{"first_name":"M.","full_name":"Ceriotti, M.","last_name":"Ceriotti"}],"external_id":{"arxiv":["1911.01140"],"pmid":["31743021"]},"article_processing_charge":"No","title":"Iterative unbiasing of quasi-equilibrium sampling","citation":{"chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation. American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.","ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107.","mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.","apa":"Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907","ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107. doi:10.1021/acs.jctc.9b00907","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","page":"100-107","doi":"10.1021/acs.jctc.9b00907","date_published":"2019-01-14T00:00:00Z","date_created":"2021-07-19T06:56:45Z","year":"2019","day":"14","publication":"Journal of Chemical Theory and Computation","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"date_updated":"2021-08-09T12:37:37Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"9680","issue":"1","volume":16,"publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1911.01140","open_access":"1"}],"month":"01","intvolume":" 16","abstract":[{"text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality.","lang":"eng"}],"oa_version":"Preprint","pmid":1},{"title":"High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment","article_processing_charge":"No","author":[{"first_name":"Marc","last_name":"Girona‐Mata","full_name":"Girona‐Mata, Marc"},{"full_name":"Miles, Evan S.","last_name":"Miles","first_name":"Evan S."},{"full_name":"Ragettli, Silvan","last_name":"Ragettli","first_name":"Silvan"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772.","ieee":"M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical Union, pp. 6754–6772, 2019.","apa":"Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019). High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2019wr024935","ama":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935","mla":"Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935.","ista":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 55(8), 6754–6772.","chicago":"Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research. American Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935."},"date_created":"2023-02-20T08:12:59Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1029/2019wr024935","page":"6754-6772","publication":"Water Resources Research","day":"01","year":"2019","oa":1,"publisher":"American Geophysical Union","quality_controlled":"1","extern":"1","date_updated":"2023-02-28T12:14:18Z","keyword":["Water Science and Technology"],"status":"public","article_type":"original","type":"journal_article","_id":"12600","volume":55,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"intvolume":" 55","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2019WR024935"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The snow cover dynamics of High Mountain Asia are usually assessed at spatial resolutions of 250 m or greater, but this scale is too coarse to clearly represent the rugged topography common to the region. Higher-resolution measurement of snow-covered area often results in biased sampling due to cloud cover and deep shadows. We therefore develop a Normalized Difference Snow Index-based workflow to delineate snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning 1999 to 2013. For each scene, we determine the spatial distribution of snow line altitudes (SLAs) with respect to aspect and across six subcatchments. Our results show that the mean SLA exhibits distinct seasonal behavior based on aspect and subcatchment position. We find that SLA dynamics respond to spatial and seasonal trade-offs in precipitation, temperature, and solar radiation, which act as primary controls. We identify two SLA spatial gradients, which we attribute to the effect of spatially variable precipitation. Our results also reveal that aspect-related SLA differences vary seasonally and are influenced by solar radiation. In terms of seasonal dominant controls, we demonstrate that the snow line is controlled by snow precipitation in winter, melt in premonsoon, a combination of both in postmonsoon, and temperature in monsoon, explaining to a large extent the spatial and seasonal variability of the SLA in the upper Langtang Valley. We conclude that while SLA and snow-covered area are complementary metrics, the SLA has a strong potential for understanding local-scale snow cover dynamics and their controlling mechanisms."}]},{"oa":1,"quality_controlled":"1","publisher":"Frontiers Media","year":"2019","publication":"Frontiers in Earth Science","day":"04","date_created":"2023-02-20T08:13:08Z","doi":"10.3389/feart.2019.00143","date_published":"2019-06-04T00:00:00Z","article_number":"143","citation":{"ieee":"R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers in Earth Science, vol. 7. Frontiers Media, 2019.","short":"R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari, A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W. Immerzeel, Frontiers in Earth Science 7 (2019).","apa":"Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari, S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143","ama":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143","mla":"Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143.","ista":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 7, 143.","chicago":"Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media, 2019. https://doi.org/10.3389/feart.2019.00143."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"René R.","full_name":"Wijngaard, René R.","last_name":"Wijngaard"},{"first_name":"Jakob F.","full_name":"Steiner, Jakob F.","last_name":"Steiner"},{"first_name":"Philip D. A.","last_name":"Kraaijenbrink","full_name":"Kraaijenbrink, Philip D. A."},{"last_name":"Klug","full_name":"Klug, Christoph","first_name":"Christoph"},{"first_name":"Surendra","full_name":"Adhikari, Surendra","last_name":"Adhikari"},{"first_name":"Argha","last_name":"Banerjee","full_name":"Banerjee, Argha"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"first_name":"Ludovicus P. H.","last_name":"van Beek","full_name":"van Beek, Ludovicus P. H."},{"full_name":"Bierkens, Marc F. P.","last_name":"Bierkens","first_name":"Marc F. P."},{"first_name":"Arthur F.","full_name":"Lutz, Arthur F.","last_name":"Lutz"},{"last_name":"Immerzeel","full_name":"Immerzeel, Walter W.","first_name":"Walter W."}],"title":"Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age","abstract":[{"text":"This study aims at developing and applying a spatially-distributed coupled glacier mass balance and ice-flow model to attribute the response of glaciers to natural and anthropogenic climate change. We focus on two glaciers with contrasting surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal) and a clean-ice glacier (Hintereisferner in Austria). The model is applied from the end of the Little Ice Age (1850) to the present-day (2016) and is forced with four bias-corrected General Circulation Models (GCMs) from the historical experiment of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet, cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic climate change on glacier mass balance and flow runs from these GCMs with and without further anthropogenic forcing after 1970 until 2016 are selected. The outcomes indicate that both glaciers experience the largest reduction in area and volume under warm climate conditions, whereas area and volume reductions are smaller under cold climate conditions. Simultaneously with changes in glacier area and volume, surface velocities generally decrease over time. Without further anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in glacier area (volume) for the clean-ice glacier. The difference in the magnitude between the two glaciers can mainly be attributed to differences in the response time of the glaciers, where the clean-ice glacier shows a much faster response to climate change. We conclude that the response of the two glaciers can mainly be attributed to anthropogenic climate change and that the impact is larger on the clean-ice glacier. The outcomes show that the model performs well under different climate conditions and that the developed approach can be used for regional-scale glacio-hydrological modeling.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3389/feart.2019.00143","open_access":"1"}],"scopus_import":"1","intvolume":" 7","month":"06","publication_status":"published","publication_identifier":{"issn":["2296-6463"]},"language":[{"iso":"eng"}],"volume":7,"_id":"12602","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-28T12:04:48Z","extern":"1"},{"date_updated":"2023-02-28T12:11:07Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"12601","issue":"252","volume":65,"publication_status":"published","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1017/jog.2019.40","open_access":"1"}],"scopus_import":"1","intvolume":" 65","month":"08","abstract":[{"text":"Ice cliffs and ponds on debris-covered glaciers have received increased attention due to their role in amplifying local melt. However, very few studies have looked at these features on the catchment scale to determine their patterns and changes in space and time. We have compiled a detailed inventory of cliffs and ponds in the Langtang catchment, central Himalaya, from six high-resolution satellite orthoimages and DEMs between 2006 and 2015, and a historic orthophoto from 1974. Cliffs cover between 1.4% (± 0.4%) in the dry and 3.4% (± 0.9%) in the wet seasons and ponds between 0.6% (± 0.1%) and 1.6% (± 0.3%) of the total debris-covered tongues. We find large variations between seasons, as cliffs and ponds tend to grow in the wetter monsoon period, but there is no obvious trend in total area over the study period. The inventory further shows that cliffs are predominately north-facing irrespective of the glacier flow direction. Both cliffs and ponds appear in higher densities several hundred metres from the terminus in areas where tributaries reach the main glacier tongue. On the largest glacier in the catchment ~10% of all cliffs and ponds persisted over nearly a decade.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"JAKOB F.","full_name":"STEINER, JAKOB F.","last_name":"STEINER"},{"first_name":"PASCAL","full_name":"BURI, PASCAL","last_name":"BURI"},{"full_name":"MILES, EVAN S.","last_name":"MILES","first_name":"EVAN S."},{"first_name":"SILVAN","last_name":"RAGETTLI","full_name":"RAGETTLI, SILVAN"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"title":"Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics","citation":{"chicago":"STEINER, JAKOB F., PASCAL BURI, EVAN S. MILES, SILVAN RAGETTLI, and Francesca Pellicciotti. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology. Cambridge University Press, 2019. https://doi.org/10.1017/jog.2019.40.","ista":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. 2019. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 65(252), 617–632.","mla":"STEINER, JAKOB F., et al. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology, vol. 65, no. 252, Cambridge University Press, 2019, pp. 617–32, doi:10.1017/jog.2019.40.","short":"J.F. STEINER, P. BURI, E.S. MILES, S. RAGETTLI, F. Pellicciotti, Journal of Glaciology 65 (2019) 617–632.","ieee":"J. F. STEINER, P. BURI, E. S. MILES, S. RAGETTLI, and F. Pellicciotti, “Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics,” Journal of Glaciology, vol. 65, no. 252. Cambridge University Press, pp. 617–632, 2019.","apa":"STEINER, J. F., BURI, P., MILES, E. S., RAGETTLI, S., & Pellicciotti, F. (2019). Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2019.40","ama":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 2019;65(252):617-632. doi:10.1017/jog.2019.40"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"617-632","date_created":"2023-02-20T08:13:03Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1017/jog.2019.40","year":"2019","publication":"Journal of Glaciology","day":"01","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press"},{"volume":8,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_id":"12525","creator":"alisjak","file_size":2493837,"date_updated":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf","date_created":"2023-02-07T09:42:46Z"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"intvolume":" 8","month":"05","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"file_date_updated":"2023-02-07T09:42:46Z","department":[{"_id":"XiFe"}],"ddc":["580"],"extern":"1","date_updated":"2023-05-08T10:54:12Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"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","_id":"12192","date_created":"2023-01-16T09:17:21Z","date_published":"2019-05-28T00:00:00Z","doi":"10.7554/elife.42530","publication":"eLife","day":"28","year":"2019","has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications, Ltd","quality_controlled":"1","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","article_processing_charge":"No","external_id":{"unknown":["31135340"]},"author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530."},"article_number":"42530"},{"article_processing_charge":"No","external_id":{"pmid":["31378616"]},"author":[{"first_name":"Emma J.","last_name":"Lawrence","full_name":"Lawrence, Emma J."},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"full_name":"Tock, Andrew J.","last_name":"Tock","first_name":"Andrew J."},{"last_name":"Lambing","full_name":"Lambing, Christophe","first_name":"Christophe"},{"full_name":"Blackwell, Alexander R.","last_name":"Blackwell","first_name":"Alexander R."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Ian R.","last_name":"Henderson","full_name":"Henderson, Ian R."}],"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","citation":{"apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2676-2686.e3","date_created":"2023-01-16T09:16:33Z","doi":"10.1016/j.cub.2019.06.084","date_published":"2019-08-19T00:00:00Z","year":"2019","publication":"Current Biology","day":"19","quality_controlled":"1","publisher":"Elsevier BV","acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:54:54Z","extern":"1","article_type":"original","type":"journal_article","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"status":"public","_id":"12190","issue":"16","volume":29,"publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 29","month":"08","abstract":[{"text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.","lang":"eng"}],"pmid":1,"oa_version":"None"},{"article_number":"2019/1015","_id":"8305","status":"public","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-10T09:27:54Z","citation":{"mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015.","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, n.d.","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015."},"title":"Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"KOKORIS KOGIAS, Eleftherios","last_name":"KOKORIS KOGIAS"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"},{"full_name":"Malkhi, Dahlia","last_name":"Malkhi","first_name":"Dahlia"},{"full_name":"Abraham, Ittai","last_name":"Abraham","first_name":"Ittai"}],"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25."},"title":"Is Debian suitable for running an HPC Cluster?","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:27:09Z","author":[{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","full_name":"Kiss, Janos"},{"last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"}],"article_processing_charge":"No","_id":"12901","status":"public","type":"conference_abstract","conference":{"start_date":"2019-02-25","location":"Grundlsee, Austria","end_date":"2019-02-27","name":"AHPC: Austrian HPC Meeting"}},{"date_updated":"2023-05-31T06:36:22Z","ddc":["570"],"extern":"1","file_date_updated":"2022-04-08T08:18:01Z","_id":"11060","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","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-04-08T08:18:01Z","file_size":6984654,"creator":"dernst","date_created":"2022-04-08T08:18:01Z","file_name":"2019_eLife_Buchwalter.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","file_id":"11138","success":1}],"volume":8,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13079"}]},"abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"10","citation":{"short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 2019;8. doi:10.7554/elife.49796","mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8, e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796.","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.49796."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","external_id":{"pmid":["31599721"]},"article_processing_charge":"No","author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"first_name":"Hsiao","last_name":"Tsai","full_name":"Tsai, Hsiao"},{"full_name":"Capitanio, Juliana","last_name":"Capitanio","first_name":"Juliana"},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","article_number":"e49796","year":"2019","has_accepted_license":"1","publication":"eLife","day":"10","date_created":"2022-04-07T07:45:02Z","doi":"10.7554/elife.49796","date_published":"2019-10-10T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications"},{"status":"public","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)"},"type":"research_data_reference","_id":"13079","title":"Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","article_processing_charge":"No","author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"last_name":"Tsai","full_name":"Tsai, Hsiao","first_name":"Hsiao"},{"full_name":"Capitanio, Juliana","last_name":"Capitanio","first_name":"Juliana"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Buchwalter, Abigail, et al. Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress. Dryad, 2019, doi:10.5061/DRYAD.N0R525H.","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. 2019. doi:10.5061/DRYAD.N0R525H","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. Dryad. https://doi.org/10.5061/DRYAD.N0R525H","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, (2019).","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress.” Dryad, 2019.","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress, Dryad, 10.5061/DRYAD.N0R525H."},"date_updated":"2023-05-31T06:36:23Z","month":"10","main_file_link":[{"url":"https://doi.org/10.5061/dryad.n0r525h","open_access":"1"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs."}],"date_created":"2023-05-23T17:09:30Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","doi":"10.5061/DRYAD.N0R525H","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11060"}]},"date_published":"2019-10-28T00:00:00Z","day":"28","year":"2019"},{"acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","oa_version":"Published Version","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"month":"08","main_file_link":[{"open_access":"1","url":"https://cccg.ca/proceedings/2019/proceedings.pdf"}],"oa":1,"publisher":"Canadian Conference on Computational Geometry","quality_controlled":"1","scopus_import":"1","publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2019","date_created":"2019-11-04T16:46:11Z","related_material":{"record":[{"relation":"extended_version","id":"8317","status":"public"}]},"date_published":"2019-08-01T00:00:00Z","page":"164-170","_id":"6989","status":"public","conference":{"name":"CCCG: Canadian Conference in Computational Geometry","start_date":"2019-08-08","end_date":"2019-08-10","location":"Edmonton, Canada"},"type":"conference","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-08-04T10:57:42Z","citation":{"mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170.","ieee":"O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170."},"department":[{"_id":"HeEd"}],"title":"Folding polyominoes with holes into a cube","external_id":{"arxiv":["1910.09917"]},"article_processing_charge":"No","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"first_name":"Hugo A","full_name":"Akitaya, Hugo A","last_name":"Akitaya"},{"first_name":"Kenneth C","full_name":"Cheung, Kenneth C","last_name":"Cheung"},{"first_name":"Erik D","last_name":"Demaine","full_name":"Demaine, Erik D"},{"last_name":"Demaine","full_name":"Demaine, Martin L","first_name":"Martin L"},{"full_name":"Fekete, Sandor P","last_name":"Fekete","first_name":"Sandor P"},{"first_name":"Linda","full_name":"Kleist, Linda","last_name":"Kleist"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"first_name":"Maarten","full_name":"Löffler, Maarten","last_name":"Löffler"},{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová"},{"first_name":"Klara","full_name":"Mundilova, Klara","last_name":"Mundilova"},{"full_name":"Schmidt, Christiane","last_name":"Schmidt","first_name":"Christiane"}]},{"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"status":"public","type":"journal_article","article_type":"original","_id":"13366","extern":"1","date_updated":"2023-08-07T10:23:41Z","intvolume":" 32","month":"11","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The ability to reversibly assemble nanoparticles using light is both fundamentally interesting and important for applications ranging from reversible data storage to controlled drug delivery. Here, the diverse approaches that have so far been developed to control the self-assembly of nanoparticles using light are reviewed and compared. These approaches include functionalizing nanoparticles with monolayers of photoresponsive molecules, placing them in photoresponsive media capable of reversibly protonating the particles under light, and decorating plasmonic nanoparticles with thermoresponsive polymers, to name just a few. The applicability of these methods to larger, micrometer-sized particles is also discussed. Finally, several perspectives on further developments in the field are offered."}],"volume":32,"issue":"20","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"article_number":"1905866","title":"The many ways to assemble nanoparticles using light","article_processing_charge":"No","external_id":{"pmid":["31709655"]},"author":[{"last_name":"Bian","full_name":"Bian, Tong","first_name":"Tong"},{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bian, Tong, et al. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials, vol. 32, no. 20, 1905866, Wiley, 2019, doi:10.1002/adma.201905866.","apa":"Bian, T., Chu, Z., & Klajn, R. (2019). The many ways to assemble nanoparticles using light. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201905866","ama":"Bian T, Chu Z, Klajn R. The many ways to assemble nanoparticles using light. Advanced Materials. 2019;32(20). doi:10.1002/adma.201905866","ieee":"T. Bian, Z. Chu, and R. Klajn, “The many ways to assemble nanoparticles using light,” Advanced Materials, vol. 32, no. 20. Wiley, 2019.","short":"T. Bian, Z. Chu, R. Klajn, Advanced Materials 32 (2019).","chicago":"Bian, Tong, Zonglin Chu, and Rafal Klajn. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials. Wiley, 2019. https://doi.org/10.1002/adma.201905866.","ista":"Bian T, Chu Z, Klajn R. 2019. The many ways to assemble nanoparticles using light. Advanced Materials. 32(20), 1905866."},"quality_controlled":"1","publisher":"Wiley","date_created":"2023-08-01T09:37:26Z","doi":"10.1002/adma.201905866","date_published":"2019-11-19T00:00:00Z","publication":"Advanced Materials","day":"19","year":"2019"},{"publisher":"American Chemical Society","quality_controlled":"1","publication":"Journal of the American Chemical Society","day":"06","year":"2019","date_created":"2023-08-01T09:39:19Z","date_published":"2019-02-06T00:00:00Z","doi":"10.1021/jacs.8b09638","page":"1949-1960","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 141(5), 1949–1960.","chicago":"Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09638.","ieee":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control of azobenzene switching on nanoparticles,” Journal of the American Chemical Society, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019.","short":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American Chemical Society 141 (2019) 1949–1960.","ama":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 2019;141(5):1949-1960. doi:10.1021/jacs.8b09638","apa":"Chu, Z., Han, Y., Bian, T., De, S., Král, P., & Klajn, R. (2019). Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09638","mla":"Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society, vol. 141, no. 5, American Chemical Society, 2019, pp. 1949–60, doi:10.1021/jacs.8b09638."},"title":"Supramolecular control of azobenzene switching on nanoparticles","article_processing_charge":"No","external_id":{"pmid":["30595017"]},"author":[{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"last_name":"Han","full_name":"Han, Yanxiao","first_name":"Yanxiao"},{"last_name":"Bian","full_name":"Bian, Tong","first_name":"Tong"},{"full_name":"De, Soumen","last_name":"De","first_name":"Soumen"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments."}],"intvolume":" 141","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"volume":141,"issue":"5","_id":"13373","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-07T10:51:12Z"},{"title":"Stimuli-responsive self-assembly of nanoparticles","external_id":{"pmid":["30688963"]},"article_processing_charge":"No","author":[{"full_name":"Grzelczak, Marek","last_name":"Grzelczak","first_name":"Marek"},{"last_name":"Liz-Marzán","full_name":"Liz-Marzán, Luis M.","first_name":"Luis M."},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Grzelczak, M., Liz-Marzán, L. M., & Klajn, R. (2019). Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c8cs00787j","ama":"Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 2019;48(5):1342-1361. doi:10.1039/c8cs00787j","ieee":"M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly of nanoparticles,” Chemical Society Reviews, vol. 48, no. 5. Royal Society of Chemistry, pp. 1342–1361, 2019.","short":"M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 1342–1361.","mla":"Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews, vol. 48, no. 5, Royal Society of Chemistry, 2019, pp. 1342–61, doi:10.1039/c8cs00787j.","ista":"Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361.","chicago":"Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8cs00787j."},"oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","date_created":"2023-08-01T09:38:52Z","date_published":"2019-01-28T00:00:00Z","doi":"10.1039/c8cs00787j","page":"1342-1361","publication":"Chemical Society Reviews","day":"28","year":"2019","keyword":["General Chemistry"],"status":"public","type":"journal_article","article_type":"original","_id":"13372","extern":"1","date_updated":"2023-08-07T10:48:31Z","intvolume":" 48","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C8CS00787J"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.","lang":"eng"}],"volume":48,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]}},{"volume":15,"publication_identifier":{"eissn":["1860-5397"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3762/bjoc.15.232","open_access":"1"}],"month":"10","intvolume":" 15","abstract":[{"lang":"eng","text":"Arylazopyrazoles represent a new family of molecular photoswitches characterized by a near-quantitative conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography have independently demonstrated that each cage can encapsulate two molecules of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage."}],"oa_version":"Published Version","pmid":1,"date_updated":"2023-08-07T10:34:56Z","extern":"1","type":"journal_article","article_type":"original","status":"public","keyword":["Organic Chemistry"],"_id":"13369","page":"2398-2407","date_published":"2019-10-10T00:00:00Z","doi":"10.3762/bjoc.15.232","date_created":"2023-08-01T09:38:06Z","year":"2019","day":"10","publication":"Beilstein Journal of Organic Chemistry","publisher":"Beilstein Institut","quality_controlled":"1","oa":1,"author":[{"full_name":"Hanopolskyi, Anton I","last_name":"Hanopolskyi","first_name":"Anton I"},{"last_name":"De","full_name":"De, Soumen","first_name":"Soumen"},{"first_name":"Michał J","last_name":"Białek","full_name":"Białek, Michał J"},{"last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael","first_name":"Yael"},{"full_name":"Avram, Liat","last_name":"Avram","first_name":"Liat"},{"first_name":"Moran","full_name":"Feller, Moran","last_name":"Feller"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"article_processing_charge":"No","external_id":{"pmid":["31666874"]},"title":"Reversible switching of arylazopyrazole within a metal–organic cage","citation":{"ista":"Hanopolskyi AI, De S, Białek MJ, Diskin-Posner Y, Avram L, Feller M, Klajn R. 2019. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 15, 2398–2407.","chicago":"Hanopolskyi, Anton I, Soumen De, Michał J Białek, Yael Diskin-Posner, Liat Avram, Moran Feller, and Rafal Klajn. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry. Beilstein Institut, 2019. https://doi.org/10.3762/bjoc.15.232.","apa":"Hanopolskyi, A. I., De, S., Białek, M. J., Diskin-Posner, Y., Avram, L., Feller, M., & Klajn, R. (2019). Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.15.232","ama":"Hanopolskyi AI, De S, Białek MJ, et al. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 2019;15:2398-2407. doi:10.3762/bjoc.15.232","short":"A.I. Hanopolskyi, S. De, M.J. Białek, Y. Diskin-Posner, L. Avram, M. Feller, R. Klajn, Beilstein Journal of Organic Chemistry 15 (2019) 2398–2407.","ieee":"A. I. Hanopolskyi et al., “Reversible switching of arylazopyrazole within a metal–organic cage,” Beilstein Journal of Organic Chemistry, vol. 15. Beilstein Institut, pp. 2398–2407, 2019.","mla":"Hanopolskyi, Anton I., et al. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry, vol. 15, Beilstein Institut, 2019, pp. 2398–407, doi:10.3762/bjoc.15.232."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"extern":"1","date_updated":"2023-08-07T10:39:34Z","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"status":"public","type":"journal_article","article_type":"original","_id":"13370","volume":19,"issue":"10","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"intvolume":" 19","month":"09","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows.","lang":"eng"}],"title":"Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules","external_id":{"pmid":["31539469"]},"article_processing_charge":"No","author":[{"first_name":"Zonglin","last_name":"Chu","full_name":"Chu, Zonglin"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chu Z, Klajn R. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 2019;19(10):7106-7111. doi:10.1021/acs.nanolett.9b02642","apa":"Chu, Z., & Klajn, R. (2019). Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b02642","short":"Z. Chu, R. Klajn, Nano Letters 19 (2019) 7106–7111.","ieee":"Z. Chu and R. Klajn, “Polysilsesquioxane nanowire networks as an ‘Artificial Solvent’ for reversible operation of photochromic molecules,” Nano Letters, vol. 19, no. 10. American Chemical Society, pp. 7106–7111, 2019.","mla":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters, vol. 19, no. 10, American Chemical Society, 2019, pp. 7106–11, doi:10.1021/acs.nanolett.9b02642.","ista":"Chu Z, Klajn R. 2019. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 19(10), 7106–7111.","chicago":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b02642."},"date_created":"2023-08-01T09:38:23Z","doi":"10.1021/acs.nanolett.9b02642","date_published":"2019-09-20T00:00:00Z","page":"7106-7111","publication":"Nano Letters","day":"20","year":"2019","quality_controlled":"1","publisher":"American Chemical Society"},{"type":"journal_article","article_type":"original","status":"public","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"_id":"13371","date_updated":"2023-08-07T10:46:50Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2019.08.012"}],"month":"09","intvolume":" 5","abstract":[{"text":"Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials.","lang":"eng"}],"oa_version":"Published Version","issue":"9","volume":5,"publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"article_processing_charge":"No","title":"Diamond grows up","citation":{"ista":"Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285.","chicago":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem. Elsevier, 2019. https://doi.org/10.1016/j.chempr.2019.08.012.","apa":"Białek, M. J., & Klajn, R. (2019). Diamond grows up. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2019.08.012","ama":"Białek MJ, Klajn R. Diamond grows up. Chem. 2019;5(9):2283-2285. doi:10.1016/j.chempr.2019.08.012","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","mla":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:10.1016/j.chempr.2019.08.012."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"2283-2285","date_published":"2019-09-12T00:00:00Z","doi":"10.1016/j.chempr.2019.08.012","date_created":"2023-08-01T09:38:38Z","year":"2019","day":"12","publication":"Chem"},{"publication_status":"published","file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:42Z","file_size":554457,"date_created":"2019-09-27T11:45:15Z","file_name":"2019_LIPIcs_Avni.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","file_id":"6913"}],"language":[{"iso":"eng"}],"volume":138,"related_material":{"record":[{"id":"9239","status":"public","relation":"later_version"}]},"ec_funded":1,"abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"08","intvolume":" 138","date_updated":"2023-08-07T14:08:34Z","ddc":["004"],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:42Z","_id":"6884","type":"conference","conference":{"start_date":"2019-08-26","end_date":"2019-08-30","location":"Aachen, Germany","name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science"},"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","has_accepted_license":"1","year":"2019","day":"01","doi":"10.4230/LIPICS.MFCS.2019.11","date_published":"2019-08-01T00:00:00Z","date_created":"2019-09-18T08:04:26Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"citation":{"ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11.","apa":"Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"external_id":{"arxiv":["1905.03835"]},"title":"Bidding mechanisms in graph games","article_number":"11","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"intvolume":" 624","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201833297"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We perform an extensive numerical study of the evolution of massive binary systems to predict the peculiar velocities that stars obtain when their companion collapses and disrupts the system. Our aim is to (i) identify which predictions are robust against model uncertainties and assess their implications, (ii) investigate which physical processes leave a clear imprint and may therefore be constrained observationally, and (iii) provide a suite of publicly available model predictions to allow for the use of kinematic constraints from the Gaia mission. We find that 22+26−8% of all massive binary systems merge prior to the first core-collapse in the system. Of the remainder, 86+11−9% become unbound because of the core-collapse. Remarkably, this rarely produces runaway stars (observationally defined as stars with velocities above 30 km s−1). These are outnumbered by more than an order of magnitude by slower unbound companions, or “walkaway stars”. This is a robust outcome of our simulations and is due to the reversal of the mass ratio prior to the explosion and widening of the orbit, as we show analytically and numerically. For stars more massive than 15 M⊙, we estimate that 10+5−8% are walkaways and only 0.5+1.0−0.4% are runaways, nearly all of which have accreted mass from their companion. Our findings are consistent with earlier studies; however, the low runaway fraction we find is in tension with observed fractions of about 10%. Thus, astrometric data on presently single massive stars can potentially constrain the physics of massive binary evolution. Finally, we show that the high end of the mass distributions of runaway stars is very sensitive to the assumed black hole natal kicks, and we propose this as a potentially stringent test for the explosion mechanism. We also discuss companions remaining bound that can evolve into X-ray and gravitational wave sources.","lang":"eng"}],"volume":624,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","article_type":"original","type":"journal_article","_id":"13471","extern":"1","date_updated":"2023-08-09T12:26:08Z","oa":1,"publisher":"EDP Sciences","quality_controlled":"1","date_created":"2023-08-03T10:14:18Z","doi":"10.1051/0004-6361/201833297","date_published":"2019-04-11T00:00:00Z","publication":"Astronomy & Astrophysics","day":"11","year":"2019","article_number":"A66","title":"Massive runaway and walkaway stars","external_id":{"arxiv":["1804.09164"]},"article_processing_charge":"No","author":[{"full_name":"Renzo, M.","last_name":"Renzo","first_name":"M."},{"first_name":"E.","last_name":"Zapartas","full_name":"Zapartas, E."},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"first_name":"S.","last_name":"Justham","full_name":"Justham, S."},{"last_name":"Farmer","full_name":"Farmer, R. J.","first_name":"R. J."},{"first_name":"R. G.","last_name":"Izzard","full_name":"Izzard, R. G."},{"last_name":"Toonen","full_name":"Toonen, S.","first_name":"S."},{"last_name":"Sana","full_name":"Sana, H.","first_name":"H."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Renzo, M., E. Zapartas, S. E. de Mink, Ylva Louise Linsdotter Götberg, S. Justham, R. J. Farmer, R. G. Izzard, S. Toonen, and H. Sana. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833297.","ista":"Renzo M, Zapartas E, de Mink SE, Götberg YLL, Justham S, Farmer RJ, Izzard RG, Toonen S, Sana H. 2019. Massive runaway and walkaway stars. Astronomy & Astrophysics. 624, A66.","mla":"Renzo, M., et al. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics, vol. 624, A66, EDP Sciences, 2019, doi:10.1051/0004-6361/201833297.","short":"M. Renzo, E. Zapartas, S.E. de Mink, Y.L.L. Götberg, S. Justham, R.J. Farmer, R.G. Izzard, S. Toonen, H. Sana, Astronomy & Astrophysics 624 (2019).","ieee":"M. Renzo et al., “Massive runaway and walkaway stars,” Astronomy & Astrophysics, vol. 624. EDP Sciences, 2019.","apa":"Renzo, M., Zapartas, E., de Mink, S. E., Götberg, Y. L. L., Justham, S., Farmer, R. J., … Sana, H. (2019). Massive runaway and walkaway stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833297","ama":"Renzo M, Zapartas E, de Mink SE, et al. Massive runaway and walkaway stars. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201833297"}},{"type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"13470","date_updated":"2023-08-09T12:29:58Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201935684"}],"scopus_import":"1","intvolume":" 627","month":"07","abstract":[{"text":"Context. Massive Wolf–Rayet (WR) stars dominate the radiative and mechanical energy budget of galaxies and probe a critical phase in the evolution of massive stars prior to core collapse. It is not known whether core He-burning WR stars (classical WR; cWR) form predominantly through wind stripping (w-WR) or binary stripping (b-WR). Whereas spectroscopy of WR binaries has so-far largely been avoided because of its complexity, our study focuses on the 44 WR binaries and binary candidates of the Large Magellanic Cloud (LMC; metallicity Z ≈ 0.5 Z⊙), which were identified on the basis of radial velocity variations, composite spectra, or high X-ray luminosities.\r\n\r\nAims. Relying on a diverse spectroscopic database, we aim to derive the physical and orbital parameters of our targets, confronting evolution models of evolved massive stars at subsolar metallicity and constraining the impact of binary interaction in forming these stars.\r\n\r\nMethods. Spectroscopy was performed using the Potsdam Wolf–Rayet (PoWR) code and cross-correlation techniques. Disentanglement was performed using the code Spectangular or the shift-and-add algorithm. Evolutionary status was interpreted using the Binary Population and Spectral Synthesis (BPASS) code, exploring binary interaction and chemically homogeneous evolution.\r\n\r\nResults. Among our sample, 28/44 objects show composite spectra and are analyzed as such. An additional five targets show periodically moving WR primaries but no detected companions (SB1); two (BAT99 99 and 112) are potential WR + compact-object candidates owing to their high X-ray luminosities. We cannot confirm the binary nature of the remaining 11 candidates. About two-thirds of the WN components in binaries are identified as cWR, and one-third as hydrogen-burning WR stars. We establish metallicity-dependent mass-loss recipes, which broadly agree with those recently derived for single WN stars, and in which so-called WN3/O3 stars are clear outliers. We estimate that 45 ± 30% of the cWR stars in our sample have interacted with a companion via mass transfer. However, only ≈12 ± 7% of the cWR stars in our sample naively appear to have formed purely owing to stripping via a companion (12% b-WR). Assuming that apparently single WR stars truly formed as single stars, this comprises ≈4% of the whole LMC WN population, which is about ten times less than expected. No obvious differences in the properties of single and binary WN stars, whose luminosities extend down to log L ≈ 5.2 [L⊙], are apparent. With the exception of a few systems (BAT99 19, 49, and 103), the equatorial rotational velocities of the OB-type companions are moderate (veq ≲ 250 km s−1) and challenge standard formalisms of angular-momentum accretion. For most objects, chemically homogeneous evolution can be rejected for the secondary, but not for the WR progenitor.\r\n\r\nConclusions. No obvious dichotomy in the locations of apparently single and binary WN stars on the Hertzsprung-Russell diagram is apparent. According to commonly used stellar evolution models (BPASS, Geneva), most apparently single WN stars could not have formed as single stars, implying that they were stripped by an undetected companion. Otherwise, it must follow that pre-WR mass-loss/mixing (e.g., during the red supergiant phase) are strongly underestimated in standard stellar evolution models.","lang":"eng"}],"oa_version":"Published Version","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1051/0004-6361/201935684e"}]},"volume":627,"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"language":[{"iso":"eng"}],"article_number":"A151","article_processing_charge":"No","author":[{"first_name":"T.","last_name":"Shenar","full_name":"Shenar, T."},{"first_name":"D. P.","last_name":"Sablowski","full_name":"Sablowski, D. P."},{"last_name":"Hainich","full_name":"Hainich, R.","first_name":"R."},{"last_name":"Todt","full_name":"Todt, H.","first_name":"H."},{"last_name":"Moffat","full_name":"Moffat, A. F. J.","first_name":"A. F. J."},{"first_name":"L. M.","full_name":"Oskinova, L. M.","last_name":"Oskinova"},{"last_name":"Ramachandran","full_name":"Ramachandran, V.","first_name":"V."},{"first_name":"H.","full_name":"Sana, H.","last_name":"Sana"},{"full_name":"Sander, A. A. C.","last_name":"Sander","first_name":"A. A. C."},{"first_name":"O.","full_name":"Schnurr, O.","last_name":"Schnurr"},{"full_name":"St-Louis, N.","last_name":"St-Louis","first_name":"N."},{"first_name":"D.","full_name":"Vanbeveren, D.","last_name":"Vanbeveren"},{"last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"full_name":"Hamann, W.-R.","last_name":"Hamann","first_name":"W.-R."}],"title":"The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud","citation":{"mla":"Shenar, T., et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics, vol. 627, A151, EDP Sciences, 2019, doi:10.1051/0004-6361/201935684.","ieee":"T. Shenar et al., “The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud,” Astronomy & Astrophysics, vol. 627. EDP Sciences, 2019.","short":"T. Shenar, D.P. Sablowski, R. Hainich, H. Todt, A.F.J. Moffat, L.M. Oskinova, V. Ramachandran, H. Sana, A.A.C. Sander, O. Schnurr, N. St-Louis, D. Vanbeveren, Y.L.L. Götberg, W.-R. Hamann, Astronomy & Astrophysics 627 (2019).","apa":"Shenar, T., Sablowski, D. P., Hainich, R., Todt, H., Moffat, A. F. J., Oskinova, L. M., … Hamann, W.-R. (2019). The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935684","ama":"Shenar T, Sablowski DP, Hainich R, et al. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 2019;627. doi:10.1051/0004-6361/201935684","chicago":"Shenar, T., D. P. Sablowski, R. Hainich, H. Todt, A. F. J. Moffat, L. M. Oskinova, V. Ramachandran, et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935684.","ista":"Shenar T, Sablowski DP, Hainich R, Todt H, Moffat AFJ, Oskinova LM, Ramachandran V, Sana H, Sander AAC, Schnurr O, St-Louis N, Vanbeveren D, Götberg YLL, Hamann W-R. 2019. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 627, A151."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"EDP Sciences","date_created":"2023-08-03T10:14:09Z","date_published":"2019-07-16T00:00:00Z","doi":"10.1051/0004-6361/201935684","year":"2019","publication":"Astronomy & Astrophysics","day":"16"},{"abstract":[{"text":"Massive stars in binaries can give rise to extreme phenomena such as X-ray binaries and gravitational wave sources after one or both stars end their lives as core-collapse supernovae. Stars in close orbit around a stellar or compact companion are expected to explode as “stripped-envelope supernovae”, showing no (Type Ib/c) or little (Type IIb) signs of hydrogen in the spectra, because hydrogen-rich progenitors are too large to fit. The physical processes responsible for the stripping process and the fate of the companion are still very poorly understood. Aiming to find new clues, we investigate Cas A, which is a very young (∼340 yr) and near (∼3.4 kpc) remnant of a core-collapse supernova. Cas A has been subject to several searches for possible companions, all unsuccessfully. We present new measurements of the proper motions and photometry of stars in the vicinity based on deep HST ACS/WFC and WFC3-IR data. We identify stellar sources that are close enough in projection but using their proper motions we show that none are compatible with being at the location of center at the time of explosion, in agreement with earlier findings. Our photometric measurements allow us to place much deeper (order-of-magnitude) upper limits on the brightness of possible undetected companions. We systematically compare them with model predictions for a wide variety of scenarios. We can confidently rule out the presence of any stellar companion of any reasonable mass and age (main sequence, pre main sequence or stripped) ruling out what many considered to be likely evolutionary scenarios for Type IIb supernova (SN IIb). More exotic scenarios that predict the presence of a compact companion (white dwarf, neutron star or black hole) are still possible as well as scenarios where the progenitor of Cas A was single at the moment of explosion (either because it was truly single, or resulted from a binary that was disrupted, or from a binary merger). The presence of a compact companion would imply that Cas A is of interest to study exotic outcomes of binary evolution. The single-at-death solution would still require fine-tuning of the process that removed most of the envelope through a mass-loss mechanism yet to be identified. We discuss how future constraints from Gaia and even deeper photometric studies may help to place further constraints.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201732206"}],"month":"03","intvolume":" 623","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":623,"_id":"13472","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"date_updated":"2023-08-09T12:28:17Z","extern":"1","quality_controlled":"1","publisher":"EDP Sciences","oa":1,"year":"2019","day":"27","publication":"Astronomy & Astrophysics","date_published":"2019-03-27T00:00:00Z","doi":"10.1051/0004-6361/201732206","date_created":"2023-08-03T10:14:27Z","article_number":"A34","citation":{"chicago":"Kerzendorf, Wolfgang E., Tuan Do, Selma E. de Mink, Ylva Louise Linsdotter Götberg, Dan Milisavljevic, Emmanouil Zapartas, Mathieu Renzo, Stephen Justham, Philipp Podsiadlowski, and Robert A. Fesen. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201732206.","ista":"Kerzendorf WE, Do T, de Mink SE, Götberg YLL, Milisavljevic D, Zapartas E, Renzo M, Justham S, Podsiadlowski P, Fesen RA. 2019. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 623, A34.","mla":"Kerzendorf, Wolfgang E., et al. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics, vol. 623, A34, EDP Sciences, 2019, doi:10.1051/0004-6361/201732206.","apa":"Kerzendorf, W. E., Do, T., de Mink, S. E., Götberg, Y. L. L., Milisavljevic, D., Zapartas, E., … Fesen, R. A. (2019). No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732206","ama":"Kerzendorf WE, Do T, de Mink SE, et al. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201732206","short":"W.E. Kerzendorf, T. Do, S.E. de Mink, Y.L.L. Götberg, D. Milisavljevic, E. Zapartas, M. Renzo, S. Justham, P. Podsiadlowski, R.A. Fesen, Astronomy & Astrophysics 623 (2019).","ieee":"W. E. Kerzendorf et al., “No surviving non-compact stellar companion to Cassiopeia A,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Wolfgang E.","last_name":"Kerzendorf","full_name":"Kerzendorf, Wolfgang E."},{"first_name":"Tuan","last_name":"Do","full_name":"Do, Tuan"},{"first_name":"Selma E.","last_name":"de Mink","full_name":"de Mink, Selma E."},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"last_name":"Milisavljevic","full_name":"Milisavljevic, Dan","first_name":"Dan"},{"full_name":"Zapartas, Emmanouil","last_name":"Zapartas","first_name":"Emmanouil"},{"full_name":"Renzo, Mathieu","last_name":"Renzo","first_name":"Mathieu"},{"full_name":"Justham, Stephen","last_name":"Justham","first_name":"Stephen"},{"full_name":"Podsiadlowski, Philipp","last_name":"Podsiadlowski","first_name":"Philipp"},{"first_name":"Robert A.","last_name":"Fesen","full_name":"Fesen, Robert A."}],"external_id":{"arxiv":["1711.00055"]},"article_processing_charge":"No","title":"No surviving non-compact stellar companion to Cassiopeia A"},{"extern":"1","date_updated":"2023-08-09T12:36:09Z","_id":"13468","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","volume":631,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class of explosions observed following the collapse of the core of massive stars. We used analytical estimates and population synthesis simulations to assess the fraction of SNe II progenitors that are expected to have exchanged mass with a companion prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history of mass exchange with a binary companion before exploding. The dominant binary channels leading to SN II progenitors involve the merger of binary stars. Mergers are expected to produce a diversity of SN II progenitor characteristics, depending on the evolutionary timing and properties of the merger. Alternatively, SN II progenitors from interacting binaries may have accreted mass from their companion, and subsequently been ejected from the binary system after their companion exploded. We show that the overall fraction of SN II progenitors that are predicted to have experienced binary interaction is robust against the main physical uncertainties in our models. However, the relative importance of different binary evolutionary channels is affected by changing physical assumptions. We further discuss ways in which binarity might contribute to the observed diversity of SNe II by considering potential observational signatures arising from each binary channel. For supernovae which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb SNe), a surviving non-compact companion would typically indicate that the supernova progenitor star was in a wide, non-interacting binary. We argue that a significant fraction of even Type II-P SNe are expected to have gained mass from a companion prior to explosion."}],"month":"11","intvolume":" 631","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201935854","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I, Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 631, A5.","chicago":"Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith, Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935854.","ieee":"E. Zapartas et al., “The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction,” Astronomy & Astrophysics, vol. 631. EDP Sciences, 2019.","short":"E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I. Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy & Astrophysics 631 (2019).","apa":"Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo, M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935854","ama":"Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 2019;631. doi:10.1051/0004-6361/201935854","mla":"Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics, vol. 631, A5, EDP Sciences, 2019, doi:10.1051/0004-6361/201935854."},"title":"The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction","author":[{"first_name":"Emmanouil","last_name":"Zapartas","full_name":"Zapartas, Emmanouil"},{"last_name":"de Mink","full_name":"de Mink, Selma E.","first_name":"Selma E."},{"last_name":"Justham","full_name":"Justham, Stephen","first_name":"Stephen"},{"full_name":"Smith, Nathan","last_name":"Smith","first_name":"Nathan"},{"last_name":"de Koter","full_name":"de Koter, Alex","first_name":"Alex"},{"last_name":"Renzo","full_name":"Renzo, Mathieu","first_name":"Mathieu"},{"full_name":"Arcavi, Iair","last_name":"Arcavi","first_name":"Iair"},{"last_name":"Farmer","full_name":"Farmer, Rob","first_name":"Rob"},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"first_name":"Silvia","full_name":"Toonen, Silvia","last_name":"Toonen"}],"article_processing_charge":"No","external_id":{"arxiv":["1907.06687"]},"article_number":"A5","day":"20","publication":"Astronomy & Astrophysics","year":"2019","doi":"10.1051/0004-6361/201935854","date_published":"2019-11-20T00:00:00Z","date_created":"2023-08-03T10:13:52Z","publisher":"EDP Sciences","quality_controlled":"1","oa":1},{"day":"17","publication":"Astronomy & Astrophysics","year":"2019","date_published":"2019-09-17T00:00:00Z","doi":"10.1051/0004-6361/201834525","date_created":"2023-08-03T10:14:00Z","publisher":"EDP Sciences","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Götberg, Ylva Louise Linsdotter, et al. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics, vol. 629, A134, EDP Sciences, 2019, doi:10.1051/0004-6361/201834525.","apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Leitherer, C., & Norman, C. (2019). The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834525","ama":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 2019;629. doi:10.1051/0004-6361/201834525","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, C. Leitherer, C. Norman, Astronomy & Astrophysics 629 (2019).","ieee":"Y. L. L. Götberg, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman, “The impact of stars stripped in binaries on the integrated spectra of stellar populations,” Astronomy & Astrophysics, vol. 629. EDP Sciences, 2019.","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834525.","ista":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. 2019. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 629, A134."},"title":"The impact of stars stripped in binaries on the integrated spectra of stellar populations","author":[{"first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg"},{"last_name":"de Mink","full_name":"de Mink, S. E.","first_name":"S. E."},{"first_name":"J. H.","full_name":"Groh, J. H.","last_name":"Groh"},{"full_name":"Leitherer, C.","last_name":"Leitherer","first_name":"C."},{"first_name":"C.","full_name":"Norman, C.","last_name":"Norman"}],"external_id":{"arxiv":["1908.06102"]},"article_processing_charge":"No","article_number":"A134","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","volume":629,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Stars stripped of their envelopes from interaction with a binary companion emit a significant fraction of their radiation as ionizing photons. They are potentially important stellar sources of ionizing radiation, however, they are still often neglected in spectral synthesis simulations or simulations of stellar feedback. In anticipating the large datasets of galaxy spectra from the upcoming James Webb Space Telescope, we modeled the radiative contribution from stripped stars by using detailed evolutionary and spectral models. We estimated their impact on the integrated spectra and specifically on the emission rates of H I-, He I-, and He II-ionizing photons from stellar populations. We find that stripped stars have the largest impact on the ionizing spectrum of a population in which star formation halted several Myr ago. In such stellar populations, stripped stars dominate the emission of ionizing photons, mimicking a younger stellar population in which massive stars are still present. Our models also suggest that stripped stars have harder ionizing spectra than massive stars. The additional ionizing radiation, with which stripped stars contribute affects observable properties that are related to the emission of ionizing photons from stellar populations. In co-eval stellar populations, the ionizing radiation from stripped stars increases the ionization parameter and the production efficiency of hydrogen ionizing photons. They also cause high values for these parameters for about ten times longer than what is predicted for massive stars. The effect on properties related to non-ionizing wavelengths is less pronounced, such as on the ultraviolet continuum slope or stellar contribution to emission lines. However, the hard ionizing radiation from stripped stars likely introduces a characteristic ionization structure of the nebula, which leads to the emission of highly ionized elements such as O2+ and C3+. We, therefore, expect that the presence of stripped stars affects the location in the BPT diagram and the diagnostic ratio of O III to O II nebular emission lines. Our models are publicly available through CDS database and on the STARBURST99 website."}],"month":"09","intvolume":" 629","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201834525"}],"extern":"1","date_updated":"2023-08-09T12:34:11Z","_id":"13469","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_type":"original","type":"journal_article"},{"publisher":"American Chemical Society ","month":"12","abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-07-27T09:51:46Z","date_published":"2019-12-19T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s001","related_material":{"record":[{"status":"public","id":"7166","relation":"used_in_publication"}]},"year":"2019","day":"19","type":"research_data_reference","status":"public","_id":"9726","article_processing_charge":"No","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"department":[{"_id":"EdHa"}],"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","date_updated":"2023-08-17T14:07:52Z","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","short":"M.C. Ucar, R. Lipowsky, (2019).","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_updated":"2023-08-22T07:40:05Z","extern":"1","_id":"14001","type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"issue":"48","volume":116,"abstract":[{"text":"Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1907189116"}],"scopus_import":"1","intvolume":" 116","month":"11","citation":{"ieee":"D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.","short":"D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.","apa":"Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116","ama":"Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116","mla":"Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116.","ista":"Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929.","chicago":"Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1906.10818"],"pmid":["31723044"]},"author":[{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Zindel, Daniel","last_name":"Zindel","first_name":"Daniel"},{"last_name":"Svoboda","full_name":"Svoboda, Vít","first_name":"Vít"},{"first_name":"Elias","full_name":"Bommeli, Elias","last_name":"Bommeli"},{"first_name":"Manuel","last_name":"Ochsner","full_name":"Ochsner, Manuel"},{"first_name":"Andres","full_name":"Tehlar, Andres","last_name":"Tehlar"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"title":"Real-time probing of chirality during a chemical reaction","year":"2019","publication":"Proceedings of the National Academy of Sciences","day":"13","page":"23923-23929","date_created":"2023-08-09T13:10:36Z","date_published":"2019-11-13T00:00:00Z","doi":"10.1073/pnas.1907189116","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"The advancement of attosecond chronoscopy has made it possible to reveal ultrashort time dynamics of photoionization [1]. Ionization delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect [2], resonances, electron correlations and transport. The extension of this approach to molecules, however, presents great challenges. In addition to the difficulty of identifying correct ionization channels, it is hard to disentangle the role of the anisotropic molecular landscape from the delays inherent to the excitation process itself. Here, we present the measurements of ionization delays from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond streaking spectroscopy, which enables to disentangle the contribution to the delay from the functional ethyl group, being responsible for the characteristic chemical reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes the molecule around the energy of the giant resonance and the released electron is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field, which yields a streaking spectrogram (see figure). Comparative phase analysis of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting overall photoemission delays for ethyl iodide. The data is recorded for multiple photon energies around the iodine 4d resonance and compared to classical Wigner propagation [3] and quantum scattering [4] calculations. Here the outgoing electron, produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby hardly influenced by the molecular potential during the birth process, acquires the necessary information about the influence of the functional ethyl group during its propagation. We find significant delay contributions that can distinguish between different functional groups, providing a sensitive probe of the local molecular environment [5]. This would stimulate to perform further angle resolved measurements in molecules to probe the potential landscape in three dimension."}],"oa_version":"None","publisher":"Institute of Electrical and Electronics Engineers","scopus_import":"1","quality_controlled":"1","month":"10","publication_identifier":{"eisbn":["9781728104690"],"isbn":["9781728104706"]},"publication_status":"published","year":"2019","day":"17","language":[{"iso":"eng"}],"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","date_published":"2019-10-17T00:00:00Z","doi":"10.1109/cleoe-eqec.2019.8871819","date_created":"2023-08-09T13:10:49Z","_id":"14002","article_number":"8871819","type":"conference","conference":{"name":"CLEO: European Conference on Lasers and Electro-Optics","location":"Munich, Germany","end_date":"2019-06-27","start_date":"2019-06-23"},"status":"public","date_updated":"2023-08-22T09:32:56Z","citation":{"chicago":"Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi, M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819.","ista":"Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L, Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: European Conference on Lasers and Electro-Optics, 8871819.","mla":"Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/cleoe-eqec.2019.8871819.","ieee":"S. Biswas et al., “Probing molecular influence on photoemission delays,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019.","short":"S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger, L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Institute of Electrical and Electronics Engineers, 2019.","apa":"Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi, M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819","ama":"Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/cleoe-eqec.2019.8871819"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Shubhadeep","last_name":"Biswas","full_name":"Biswas, Shubhadeep"},{"last_name":"Liontos","full_name":"Liontos, I.","first_name":"I."},{"first_name":"A. M.","full_name":"Kamal, A. M.","last_name":"Kamal"},{"first_name":"N. G.","last_name":"Kling","full_name":"Kling, N. G."},{"first_name":"A. F.","full_name":"Alharbi, A. F.","last_name":"Alharbi"},{"first_name":"M.","full_name":"Alharbi, M.","last_name":"Alharbi"},{"last_name":"Azzeer","full_name":"Azzeer, A. M.","first_name":"A. M."},{"first_name":"H. J.","last_name":"Worner","full_name":"Worner, H. J."},{"full_name":"Landsman, A. S.","last_name":"Landsman","first_name":"A. S."},{"last_name":"Kling","full_name":"Kling, M. F.","first_name":"M. F."},{"full_name":"Forg, B.","last_name":"Forg","first_name":"B."},{"last_name":"Schotz","full_name":"Schotz, J.","first_name":"J."},{"full_name":"Schweinberger, W.","last_name":"Schweinberger","first_name":"W."},{"first_name":"L.","full_name":"Ortmann, L.","last_name":"Ortmann"},{"last_name":"Zimmermann","full_name":"Zimmermann, T.","first_name":"T."},{"full_name":"Pi, L.-W.","last_name":"Pi","first_name":"L.-W."},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"H. A.","last_name":"Masood","full_name":"Masood, H. A."}],"article_processing_charge":"No","title":"Probing molecular influence on photoemission delays"},{"title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.","ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s41468-019-00029-8","date_created":"2019-07-24T08:37:29Z","page":"29–58","day":"01","publication":"Journal of Applied and Computational Topology","has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"Springer Nature","oa":1,"file_date_updated":"2020-07-14T12:47:36Z","department":[{"_id":"HeEd"}],"ddc":["000"],"date_updated":"2023-08-22T12:37:47Z","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":"6671","issue":"1-2","volume":3,"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6741","checksum":"a5b244db9f751221409cf09c97ee0935","creator":"dernst","file_size":2215157,"date_updated":"2020-07-14T12:47:36Z","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","date_created":"2019-07-31T08:09:56Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"publication_status":"published","month":"06","intvolume":" 3","oa_version":"Published Version","abstract":[{"text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.","lang":"eng"}]},{"external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"article_processing_charge":"No","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"first_name":"István","full_name":"Gyöngy, István","last_name":"Gyöngy"}],"title":"A Feynman–Kac formula for stochastic Dirichlet problems","citation":{"mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"995-1012","date_created":"2018-12-11T11:45:42Z","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.spa.2018.04.003","year":"2019","isi":1,"publication":"Stochastic Processes and their Applications","day":"01","oa":1,"publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:20:49Z","article_type":"original","type":"journal_article","status":"public","_id":"301","volume":129,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.04177"}],"scopus_import":"1","intvolume":" 129","month":"03","abstract":[{"lang":"eng","text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense."}],"oa_version":"Preprint"},{"issue":"2","volume":368,"ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5688","checksum":"c7e9880b43ac726712c1365e9f2f73a6","file_size":893902,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_name":"2018_CommunMathPhys_Deuchert.pdf","date_created":"2018-12-17T10:34:06Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 368","abstract":[{"lang":"eng","text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"RoSe"}],"date_updated":"2023-08-24T14:27:51Z","ddc":["530"],"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)"},"status":"public","_id":"80","page":"723-776","date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s00220-018-3239-0","date_created":"2018-12-11T11:44:31Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Communications in Mathematical Physics","quality_controlled":"1","publisher":"Springer","oa":1,"author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"publist_id":"7974","external_id":{"isi":["000467796800007"]},"article_processing_charge":"Yes (via OA deal)","title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","citation":{"chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.","ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776.","mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0.","apa":"Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}]},{"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","publication":"Trends in Ecology and Evolution","day":"01","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","title":"Evolving inversions","article_processing_charge":"No","external_id":{"isi":["000459899000013"]},"author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","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.","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","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","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","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.","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."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ec_funded":1,"issue":"3","volume":34,"language":[{"iso":"eng"}],"file":[{"file_id":"7245","checksum":"ef24572d6ebcc1452c067e05410cc4a2","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-09T10:55:58Z","file_name":"2019_Trends_Evolution_Faria.pdf","creator":"cziletti","date_updated":"2020-07-14T12:47:13Z","file_size":1946795}],"publication_status":"published","publication_identifier":{"issn":["01695347"]},"intvolume":" 34","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2023-08-24T14:29:48Z","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"},"type":"journal_article","article_type":"original","_id":"5911"},{"date_created":"2018-12-11T11:46:29Z","date_published":"2019-10-01T00:00:00Z","doi":"10.4171/JEMS/896","page":"2995-3052","publication":"Journal of the European Mathematical Society","day":"01","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"European Mathematical Society","title":"Arithmetic and representation theory of wild character varieties","article_processing_charge":"No","external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"publist_id":"7384","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Hausel, Tamas","last_name":"Hausel"},{"id":"43D735EE-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Mereb","full_name":"Mereb, Martin"},{"first_name":"Michael","full_name":"Wong, Michael","last_name":"Wong"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","apa":"Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896","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","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."},"project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"}],"ec_funded":1,"issue":"10","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1435-9855"]},"intvolume":" 21","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"scopus_import":"1","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"}],"department":[{"_id":"TaHa"}],"date_updated":"2023-08-24T14:24:49Z","status":"public","article_type":"original","type":"journal_article","_id":"439"},{"day":"01","publication":"European Journal of Human Genetics","isi":1,"year":"2019","date_published":"2019-01-01T00:00:00Z","doi":"10.1038/s41431-018-0231-2","date_created":"2018-12-11T11:44:39Z","page":"161-166","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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."},"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","author":[{"first_name":"Ashley","full_name":"Marsh, Ashley","last_name":"Marsh"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"},{"first_name":"Paul","last_name":"Lockhart","full_name":"Lockhart, Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"publist_id":"7949","external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","volume":27,"oa_version":"Published Version","pmid":1,"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."}],"month":"01","intvolume":" 27","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"date_updated":"2023-08-24T14:28:24Z","department":[{"_id":"GaNo"}],"_id":"105","status":"public","type":"journal_article","article_type":"original"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012","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","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."},"title":"Entropy solutions for stochastic porous media equations","external_id":{"isi":["000456332500026"],"arxiv":["1803.06953"]},"article_processing_charge":"No","author":[{"first_name":"Konstantinos","last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos"},{"last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate"},{"first_name":"Benjamin","full_name":"Gess, Benjamin","last_name":"Gess"}],"publist_id":"7989","publication":"Journal of Differential Equations","day":"5","year":"2019","isi":1,"date_created":"2018-12-11T11:44:26Z","doi":"10.1016/j.jde.2018.09.012","date_published":"2019-03-05T00:00:00Z","page":"3732-3763","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-08-24T14:30:16Z","department":[{"_id":"JaMa"}],"_id":"65","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","volume":266,"issue":"6","oa_version":"Preprint","abstract":[{"text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.","lang":"eng"}],"intvolume":" 266","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"scopus_import":"1"},{"_id":"5907","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","date_updated":"2023-08-24T14:33:16Z","ddc":["580"],"department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:13Z","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"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"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,"file_id":"5923","checksum":"4129c7d7663d1f8a1edf8c4232372f66","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":9,"issue":"1","article_number":"331","citation":{"mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","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.","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000456392400012"]},"author":[{"first_name":"Réka","full_name":"Mócsai, Réka","last_name":"Mócsai"},{"full_name":"Figl, Rudolf","last_name":"Figl","first_name":"Rudolf"},{"first_name":"Clemens","full_name":"Troschl, Clemens","last_name":"Troschl"},{"full_name":"Strasser, Richard","last_name":"Strasser","first_name":"Richard"},{"first_name":"Elisabeth","full_name":"Svehla, Elisabeth","last_name":"Svehla"},{"first_name":"Markus","full_name":"Windwarder, Markus","last_name":"Windwarder"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","last_name":"Thader"},{"first_name":"Friedrich","full_name":"Altmann, Friedrich","last_name":"Altmann"}],"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2019","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"23","date_created":"2019-02-03T22:59:13Z","doi":"10.1038/s41598-018-36884-1","date_published":"2019-01-23T00:00:00Z"},{"quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"isi":1,"year":"2019","day":"22","publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"1420-1429","date_published":"2019-01-22T00:00:00Z","doi":"10.1073/pnas.1818099116","date_created":"2019-02-03T22:59:14Z","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","author":[{"last_name":"Lee","full_name":"Lee, Eunkyoung","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"},{"full_name":"Benitez-Fuente, Francisco","last_name":"Benitez-Fuente","first_name":"Francisco"},{"first_name":"Matthew","last_name":"Strelau","full_name":"Strelau, Matthew"},{"first_name":"Alberto P.","full_name":"Macho, Alberto P.","last_name":"Macho"},{"first_name":"Miguel A.","full_name":"Botella, Miguel A.","last_name":"Botella"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Abel","full_name":"Rosado, Abel","last_name":"Rosado"}],"article_processing_charge":"No","external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"month":"01","intvolume":" 116","publication_status":"published","language":[{"iso":"eng"}],"volume":116,"issue":"4","_id":"5908","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:31:09Z","department":[{"_id":"JiFr"}]},{"external_id":{"isi":["000463802800009"]},"article_processing_charge":"No","author":[{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"first_name":"Monique","full_name":"Burrus, Monique","last_name":"Burrus"},{"first_name":"Sandrine","last_name":"Paute","full_name":"Paute, Sandrine"},{"first_name":"Christine","full_name":"Lauzeral, Christine","last_name":"Lauzeral"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"}],"title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","citation":{"short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"80-92","date_created":"2018-12-16T22:59:20Z","date_published":"2019-01-01T00:00:00Z","doi":"10.1080/23818107.2018.1545142","year":"2019","isi":1,"publication":"Botany Letters","day":"01","publisher":"Taylor and Francis","quality_controlled":"1","department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:34:12Z","type":"journal_article","status":"public","_id":"5680","issue":"1","volume":166,"publication_status":"published","publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 166","month":"01","abstract":[{"lang":"eng","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."}],"oa_version":"None"},{"date_published":"2019-08-01T00:00:00Z","doi":"10.1002/jgt.22436","date_created":"2018-12-30T22:59:15Z","page":"365-394","day":"01","publication":"Journal of Graph Theory","isi":1,"year":"2019","quality_controlled":"1","publisher":"Wiley","oa":1,"title":"Extending partial representations of circle graphs","author":[{"first_name":"Steven","full_name":"Chaplick, Steven","last_name":"Chaplick"},{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Klavík, Pavel","last_name":"Klavík","first_name":"Pavel"}],"article_processing_charge":"No","external_id":{"arxiv":["1309.2399"],"isi":["000485392800004"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"volume":91,"issue":"4","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03649024"]},"publication_status":"published","month":"08","intvolume":" 91","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1309.2399","open_access":"1"}],"oa_version":"Preprint","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"}],"department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:30:43Z","status":"public","type":"journal_article","article_type":"original","_id":"5790"},{"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,"publisher":"Elsevier","quality_controlled":"1","year":"2019","isi":1,"publication":"Linear Algebra and Its Applications","day":"01","page":"67-78","date_created":"2018-12-11T11:46:17Z","doi":"10.1016/j.laa.2018.03.002","date_published":"2019-09-01T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"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.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1712.05324"],"isi":["000470955300005"]},"author":[{"orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"publist_id":"7424","title":"Jointly convex quantum Jensen divergences","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"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1712.05324","open_access":"1"}],"scopus_import":"1","intvolume":" 576","month":"09","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":576,"_id":"405","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:31:47Z","department":[{"_id":"LaEr"}]},{"publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":371,"issue":"8","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"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01999"}],"month":"04","intvolume":" 371","date_updated":"2023-08-24T14:34:56Z","department":[{"_id":"TiBr"}],"_id":"175","type":"journal_article","status":"public","isi":1,"year":"2019","day":"15","publication":"Transactions of the American Mathematical Society","page":"5757-5785","doi":"10.1090/tran/7514","date_published":"2019-04-15T00:00:00Z","date_created":"2018-12-11T11:45:01Z","publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"citation":{"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.","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","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","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.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publist_id":"7746","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"full_name":"Loughran, Daniel","last_name":"Loughran","first_name":"Daniel"}],"article_processing_charge":"No","external_id":{"isi":["000464034200019"],"arxiv":["1705.01999"]},"title":"Sieving rational points on varieties"},{"title":"Singular SPDEs in domains with boundaries","external_id":{"isi":["000463613800001"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"7546","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"last_name":"Hairer","full_name":"Hairer, Martin","first_name":"Martin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","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.","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","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","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.","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","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."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2018-12-11T11:45:48Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1007/s00440-018-0841-1","page":"697–758","publication":"Probability Theory and Related Fields","day":"01","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:46:03Z","ddc":["510"],"date_updated":"2023-08-24T14:38:32Z","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","_id":"319","issue":"3-4","volume":173,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:03Z","file_size":893182,"creator":"dernst","date_created":"2018-12-17T16:25:24Z","file_name":"2018_ProbTheory_Gerencser.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5722","checksum":"288d16ef7291242f485a9660979486e3"}],"publication_status":"published","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"intvolume":" 173","month":"04","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."}]},{"title":"Stability of the matrix Dyson equation and random matrices with correlations","publist_id":"7394","author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"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","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"}],"external_id":{"isi":["000459396500007"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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."},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"doi":"10.1007/s00440-018-0835-z","date_published":"2019-02-01T00:00:00Z","date_created":"2018-12-11T11:46:25Z","page":"293–373","day":"01","publication":"Probability Theory and Related Fields","has_accepted_license":"1","isi":1,"year":"2019","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-08-24T14:39:00Z","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":"429","volume":173,"issue":"1-2","ec_funded":1,"file":[{"file_id":"5720","checksum":"f9354fa5c71f9edd17132588f0dc7d01","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_ProbTheory_Ajanki.pdf","date_created":"2018-12-17T16:12:08Z","creator":"dernst","file_size":1201840,"date_updated":"2020-07-14T12:46:26Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"publication_status":"published","month":"02","intvolume":" 173","scopus_import":"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."}]},{"_id":"5947","status":"public","type":"conference","conference":{"name":"ICDCN: Conference on Distributed Computing and Networking","start_date":"2019-01-04","end_date":"2019-01-07","location":"Bangalore, India"},"date_updated":"2023-08-24T14:41:53Z","department":[{"_id":"DaAl"}],"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","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617","ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.","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.","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."},"title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","author":[{"id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi"},{"first_name":"Sathya","last_name":"Peri","full_name":"Peri, Sathya"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"},{"full_name":"Singhal, Nandini","last_name":"Singhal","first_name":"Nandini"}],"article_processing_charge":"No","external_id":{"isi":["000484491600019"],"arxiv":["1809.00896"]},"quality_controlled":"1","publisher":"ACM","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"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"isi":1,"year":"2019","day":"30","publication":"Discrete Applied Mathematics","page":"266-231","date_published":"2019-04-30T00:00:00Z","doi":"10.1016/j.dam.2018.12.025","date_created":"2019-01-20T22:59:17Z","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"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.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","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","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"article_processing_charge":"No","external_id":{"arxiv":["1708.08037"],"isi":["000466061100020"]},"title":"Thrackles: An improved upper bound","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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"month":"04","intvolume":" 259","publication_identifier":{"issn":["0166218X"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"433","status":"public"}]},"volume":259,"issue":"4","_id":"5857","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:39:33Z","department":[{"_id":"UlWa"}]},{"article_number":"9","title":"Thermodynamics of duplication thresholds in synthetic protocell systems","external_id":{"isi":["000464125500001"]},"article_processing_charge":"No","author":[{"last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009."},"oa":1,"quality_controlled":"1","publisher":"MDPI","date_created":"2019-02-10T22:59:15Z","date_published":"2019-01-15T00:00:00Z","doi":"10.3390/life9010009","publication":"Life","day":"15","year":"2019","has_accepted_license":"1","isi":1,"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","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-08-24T14:43:41Z","intvolume":" 9","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":9,"issue":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-11T10:45:27Z","file_name":"2019_Life_Corominas.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_size":963454,"checksum":"7d2322cd96ace41959909b66702d5cf4","file_id":"5951","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["20751729"]}},{"day":"24","publication":"Frontiers in Chemistry","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-01-24T00:00:00Z","doi":"10.3389/fchem.2018.00655","date_created":"2019-02-17T22:59:24Z","quality_controlled":"1","publisher":"Frontiers Media S.A.","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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).","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."},"title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","author":[{"first_name":"Marco","last_name":"Lindner","full_name":"Lindner, Marco"},{"full_name":"Tresztenyak, Aliz","last_name":"Tresztenyak","first_name":"Aliz"},{"full_name":"Fülöp, Gergö","last_name":"Fülöp","first_name":"Gergö"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"first_name":"Adrian","last_name":"Prinz","full_name":"Prinz, Adrian"},{"first_name":"Iris","full_name":"Prinz, Iris","last_name":"Prinz"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"first_name":"Gerhard J.","last_name":"Schütz","full_name":"Schütz, Gerhard J."},{"full_name":"Sevcsik, Eva","last_name":"Sevcsik","first_name":"Eva"}],"external_id":{"isi":["000456718000001"]},"article_processing_charge":"No","article_number":"655","file":[{"checksum":"7841301d7c53b56ef873791b4b6f7b24","file_id":"6039","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-18T15:10:34Z","file_name":"2019_frontiers_Lindner.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:17Z","file_size":1766820}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22962646"]},"publication_status":"published","volume":6,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 6","scopus_import":"1","ddc":["540"],"date_updated":"2023-08-24T14:45:38Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:47:17Z","_id":"6029","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)"}},{"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"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000475465000003"]},"title":"A solution theory for quasilinear singular SPDEs","citation":{"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","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","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.","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.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","quality_controlled":"1","oa":1,"page":"1983-2005","date_published":"2019-02-08T00:00:00Z","doi":"10.1002/cpa.21816","date_created":"2019-02-17T22:59:24Z","has_accepted_license":"1","isi":1,"year":"2019","day":"08","publication":"Communications on Pure and Applied Mathematics","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":"6028","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:17Z","date_updated":"2023-08-24T14:44:31Z","ddc":["500"],"scopus_import":"1","month":"02","intvolume":" 72","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":72,"issue":"9","publication_status":"published","file":[{"creator":"kschuh","file_size":381350,"date_updated":"2020-07-14T12:47:17Z","file_name":"2019_Wiley_Gerencser.pdf","date_created":"2020-01-07T13:25:55Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7237","checksum":"09aec427eb48c0f96a1cce9ff53f013b"}],"language":[{"iso":"eng"}]},{"oa_version":"Preprint","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"}],"month":"01","intvolume":" 11388","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":11388,"_id":"5948","status":"public","type":"conference","conference":{"name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","start_date":"2019-01-13","location":"Cascais, Portugal","end_date":"2019-01-15"},"date_updated":"2023-08-24T14:42:22Z","department":[{"_id":"KrCh"}],"quality_controlled":"1","publisher":"Springer Nature","day":"11","publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","isi":1,"year":"2019","date_published":"2019-01-11T00:00:00Z","doi":"10.1007/978-3-030-11245-5_22","date_created":"2019-02-10T22:59:17Z","page":"468-490","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, 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","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."},"title":"Termination of nondeterministic probabilistic programs","author":[{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"article_processing_charge":"No","external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]}},{"article_type":"original","type":"journal_article","status":"public","_id":"5945","department":[{"_id":"GaTk"}],"date_updated":"2023-08-24T14:42:47Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.007"}],"month":"02","intvolume":" 176","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","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/"}]},"issue":"4","volume":176,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"author":[{"first_name":"Mariela D.","full_name":"Petkova, Mariela D.","last_name":"Petkova"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"last_name":"Wieschaus","full_name":"Wieschaus, Eric F.","first_name":"Eric F."},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"article_processing_charge":"No","title":"Optimal decoding of cellular identities in a genetic network","citation":{"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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Cell Press","oa":1,"page":"844-855.e15","doi":"10.1016/j.cell.2019.01.007","date_published":"2019-02-07T00:00:00Z","date_created":"2019-02-10T22:59:16Z","isi":1,"year":"2019","day":"07","publication":"Cell"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}],"month":"03","intvolume":" 863","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":863,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"5943","department":[{"_id":"BjHo"}],"date_updated":"2023-08-24T14:43:13Z","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"page":"386-406","doi":"10.1017/jfm.2018.974","date_published":"2019-03-25T00:00:00Z","date_created":"2019-02-10T22:59:15Z","isi":1,"year":"2019","day":"25","publication":"Journal of Fluid Mechanics","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"last_name":"Klotz","full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz"},{"first_name":"Konrad","last_name":"Gumowski","full_name":"Gumowski, Konrad"},{"first_name":"José Eduardo","full_name":"Wesfreid, José Eduardo","last_name":"Wesfreid"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.07931"],"isi":["000526029100016"]},"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","citation":{"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.","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.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"volume":11427,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9998496f6fe202c0a19124b4209154c6","file_id":"6408","creator":"dernst","date_updated":"2020-07-14T12:47:17Z","file_size":773083,"date_created":"2019-05-10T14:16:05Z","file_name":"2019_LNCS_Christakis.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 11427","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."}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:17Z","ddc":["000"],"date_updated":"2023-08-24T14:47:45Z","status":"public","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":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2019-04-11","location":"Prague, Czech Republic","start_date":"2019-04-06"},"_id":"6042","date_published":"2019-04-04T00:00:00Z","doi":"10.1007/978-3-030-17462-0_13","date_created":"2019-02-18T16:44:06Z","page":"226-243","day":"04","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","isi":1,"has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"Springer Nature","oa":1,"title":"Semantic fault localization and suspiciousness ranking","author":[{"last_name":"Christakis","full_name":"Christakis, Maria","first_name":"Maria"},{"first_name":"Matthias","full_name":"Heizmann, Matthias","last_name":"Heizmann"},{"last_name":"Mansur","full_name":"Mansur, Muhammad Numair","first_name":"Muhammad Numair"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Valentin","last_name":"Wüstholz","full_name":"Wüstholz, Valentin"}],"external_id":{"isi":["000681166500013"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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."},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}]},{"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"ToHe"}],"date_updated":"2023-08-24T14:47:21Z","ddc":["000"],"type":"conference","conference":{"start_date":"2019-04-16","location":"Montreal, QC, Canada","end_date":"2019-04-18","name":"HSCC: Hybrid Systems Computation and Control"},"status":"public","keyword":["reachability analysis","hybrid systems","lazy computation"],"_id":"6035","volume":22,"ec_funded":1,"publication_identifier":{"isbn":["9781450362825"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"28ed56439aea5991c3122d4730fd828f","file_id":"6067","date_updated":"2020-07-14T12:47:17Z","file_size":3784414,"creator":"cschilli","date_created":"2019-03-05T09:27:18Z","file_name":"hscc19.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 22","abstract":[{"lang":"eng","text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems."}],"oa_version":"Submitted Version","author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"last_name":"Potomkin","full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling"}],"article_processing_charge":"No","external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"title":"JuliaReach: A toolbox for set-based reachability","citation":{"mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"page":"39-44","doi":"10.1145/3302504.3311804","date_published":"2019-04-16T00:00:00Z","date_created":"2019-02-18T14:43:28Z","has_accepted_license":"1","isi":1,"year":"2019","day":"16","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","quality_controlled":"1","publisher":"ACM","oa":1},{"author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"external_id":{"pmid":["30778205"],"isi":["000459890700008"]},"article_processing_charge":"No","title":"A practical guide to optimization in X10 expansion microscopy","citation":{"chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.","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.","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.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"832–863","date_published":"2019-03-01T00:00:00Z","doi":"10.1038/s41596-018-0117-3","date_created":"2019-02-24T22:59:20Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Nature Protocols","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"file_date_updated":"2021-06-29T14:41:46Z","department":[{"_id":"JoDa"},{"_id":"Bio"}],"date_updated":"2023-08-24T14:48:33Z","ddc":["570"],"type":"journal_article","article_type":"original","status":"public","_id":"6052","issue":"3","volume":14,"ec_funded":1,"publication_status":"published","file":[{"date_updated":"2021-06-29T14:41:46Z","file_size":84478958,"creator":"kschuh","date_created":"2021-06-29T14:41:46Z","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"open_access","relation":"main_file","file_id":"9619","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 14","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","pmid":1},{"article_number":"e42093","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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.","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.","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","last_name":"Capek","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy"},{"full_name":"Morri, Maurizio","last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"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":["000458025300001"]},"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"06","publication":"eLife","doi":"10.7554/eLife.42093","date_published":"2019-02-06T00:00:00Z","date_created":"2019-02-17T22:59:22Z","_id":"6025","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":"2023-08-24T14:46:01Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"lang":"eng","text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 8","publication_status":"published","file":[{"date_created":"2019-02-18T15:17:21Z","file_name":"2019_elife_Capek.pdf","date_updated":"2020-07-14T12:47:17Z","file_size":5500707,"creator":"dernst","file_id":"6041","checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":8,"ec_funded":1},{"title":"Genetic dissection of assortative mating behavior","external_id":{"isi":["000460317100001"]},"article_processing_charge":"No","author":[{"first_name":"Richard M.","full_name":"Merrill, Richard M.","last_name":"Merrill"},{"first_name":"Pasi","full_name":"Rastas, Pasi","last_name":"Rastas"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C"},{"first_name":"Sarah","full_name":"Barker, Sarah","last_name":"Barker"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"last_name":"Jiggins","full_name":"Jiggins, Chris D.","first_name":"Chris D."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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.","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."},"article_number":"e2005902","date_created":"2019-02-17T22:59:21Z","date_published":"2019-02-07T00:00:00Z","doi":"10.1371/journal.pbio.2005902","publication":"PLoS Biology","day":"07","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2023-08-24T14:46:23Z","status":"public","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)"},"type":"journal_article","_id":"6022","volume":17,"issue":"2","related_material":{"record":[{"relation":"research_data","status":"public","id":"9801"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"5f34001617ee729314ca520c049b1112","file_id":"6036","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-02-18T14:57:24Z","file_name":"2019_PLOS_Merrill.pdf","date_updated":"2020-07-14T12:47:17Z","file_size":2005949,"creator":"dernst"}],"publication_status":"published","intvolume":" 17","month":"02","scopus_import":"1","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."}]}]