[{"publication_status":"published","status":"public","title":"Dissection of genetic variation and evidence for pleiotropy in male pattern baldness","intvolume":" 9","publisher":"Springer Nature","_id":"7712","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:02Z","date_created":"2020-04-30T10:41:19Z","volume":9,"oa_version":"Published Version","author":[{"first_name":"Chloe X.","last_name":"Yap","full_name":"Yap, Chloe X."},{"full_name":"Sidorenko, Julia","first_name":"Julia","last_name":"Sidorenko"},{"first_name":"Yang","last_name":"Wu","full_name":"Wu, Yang"},{"first_name":"Kathryn E.","last_name":"Kemper","full_name":"Kemper, Kathryn E."},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"article_number":"5407","type":"journal_article","extern":"1","abstract":[{"text":"Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait.","lang":"eng"}],"quality_controlled":"1","article_type":"original","publication":"Nature Communications","oa":1,"citation":{"ama":"Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 2018;9. doi:10.1038/s41467-018-07862-y","ista":"Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407.","apa":"Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y","ieee":"C. X. Yap et al., “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer Nature, 2018.","mla":"Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer Nature, 2018, doi:10.1038/s41467-018-07862-y.","short":"C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018).","chicago":"Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y."},"main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-07862-y","open_access":"1"}],"language":[{"iso":"eng"}],"date_published":"2018-12-20T00:00:00Z","doi":"10.1038/s41467-018-07862-y","day":"20","month":"12","article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]}},{"author":[{"full_name":"Maier, Robert M.","last_name":"Maier","first_name":"Robert M."},{"full_name":"Zhu, Zhihong","first_name":"Zhihong","last_name":"Zhu"},{"full_name":"Lee, Sang Hong","first_name":"Sang Hong","last_name":"Lee"},{"full_name":"Trzaskowski, Maciej","last_name":"Trzaskowski","first_name":"Maciej"},{"full_name":"Ruderfer, Douglas M.","last_name":"Ruderfer","first_name":"Douglas M."},{"last_name":"Stahl","first_name":"Eli A.","full_name":"Stahl, Eli A."},{"full_name":"Ripke, Stephan","first_name":"Stephan","last_name":"Ripke"},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."},{"first_name":"Jian","last_name":"Yang","full_name":"Yang, Jian"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"volume":9,"oa_version":"Published Version","date_created":"2020-04-30T10:42:29Z","date_updated":"2021-01-12T08:15:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7716","year":"2018","publisher":"Springer Nature","intvolume":" 9","title":"Improving genetic prediction by leveraging genetic correlations among human diseases and traits","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait."}],"extern":"1","type":"journal_article","article_number":"989","date_published":"2018-03-07T00:00:00Z","doi":"10.1038/s41467-017-02769-6","language":[{"iso":"eng"}],"citation":{"chicago":"Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6.","mla":"Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications, vol. 9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6.","short":"R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl, S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications 9 (2018).","ista":"Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 9, 989.","ieee":"R. M. Maier et al., “Improving genetic prediction by leveraging genetic correlations among human diseases and traits,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02769-6","ama":"Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 2018;9. doi:10.1038/s41467-017-02769-6"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02769-6","open_access":"1"}],"publication":"Nature Communications","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","day":"07","month":"03"},{"day":"26","month":"11","article_processing_charge":"No","publication_identifier":{"issn":["2397-3374"]},"article_type":"original","quality_controlled":"1","page":"948-954","publication":"Nature Human Behaviour","citation":{"ieee":"L. Yengo et al., “Imprint of assortative mating on the human genome,” Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018.","apa":"Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3","ista":"Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. 2018. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2(12), 948–954.","ama":"Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3","chicago":"Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper, Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018. https://doi.org/10.1038/s41562-018-0476-3.","short":"L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski, J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J. Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954.","mla":"Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3."},"language":[{"iso":"eng"}],"doi":"10.1038/s41562-018-0476-3","date_published":"2018-11-26T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"text":"Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes.","lang":"eng"}],"issue":"12","status":"public","title":"Imprint of assortative mating on the human genome","publication_status":"published","intvolume":" 2","publisher":"Springer Nature","year":"2018","_id":"7715","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:03Z","date_created":"2020-04-30T10:42:12Z","volume":2,"oa_version":"None","author":[{"full_name":"Yengo, Loic","last_name":"Yengo","first_name":"Loic"},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"first_name":"Matthew C.","last_name":"Keller","full_name":"Keller, Matthew C."},{"first_name":"Kathryn E.","last_name":"Kemper","full_name":"Kemper, Kathryn E."},{"first_name":"Yuanhao","last_name":"Yang","full_name":"Yang, Yuanhao"},{"first_name":"Maciej","last_name":"Trzaskowski","full_name":"Trzaskowski, Maciej"},{"full_name":"Gratten, Jacob","first_name":"Jacob","last_name":"Gratten"},{"full_name":"Turley, Patrick","last_name":"Turley","first_name":"Patrick"},{"full_name":"Cesarini, David","first_name":"David","last_name":"Cesarini"},{"full_name":"Benjamin, Daniel J.","last_name":"Benjamin","first_name":"Daniel J."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"last_name":"Goddard","first_name":"Michael E.","full_name":"Goddard, Michael E."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}]},{"publication":"Nature Communications","oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02317-2","open_access":"1"}],"citation":{"apa":"Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang, J. (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2","ieee":"Z. Zhu et al., “Causal associations between risk factors and common diseases inferred from GWAS summary data,” Nature Communications, vol. 9. Springer Nature, 2018.","ista":"Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 9, 224.","ama":"Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 2018;9. doi:10.1038/s41467-017-02317-2","chicago":"Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2.","short":"Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson, J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018).","mla":"Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer Nature, 2018, doi:10.1038/s41467-017-02317-2."},"quality_controlled":"1","article_type":"original","doi":"10.1038/s41467-017-02317-2","date_published":"2018-01-15T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"15","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7714","year":"2018","publication_status":"published","title":"Causal associations between risk factors and common diseases inferred from GWAS summary data","status":"public","publisher":"Springer Nature","intvolume":" 9","author":[{"first_name":"Zhihong","last_name":"Zhu","full_name":"Zhu, Zhihong"},{"full_name":"Zheng, Zhili","first_name":"Zhili","last_name":"Zheng"},{"full_name":"Zhang, Futao","last_name":"Zhang","first_name":"Futao"},{"last_name":"Wu","first_name":"Yang","full_name":"Wu, Yang"},{"full_name":"Trzaskowski, Maciej","last_name":"Trzaskowski","first_name":"Maciej"},{"full_name":"Maier, Robert","last_name":"Maier","first_name":"Robert"},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"first_name":"John J.","last_name":"McGrath","full_name":"McGrath, John J."},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"full_name":"Wray, Naomi R.","first_name":"Naomi R.","last_name":"Wray"},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"}],"date_updated":"2021-01-12T08:15:03Z","date_created":"2020-04-30T10:41:55Z","oa_version":"Published Version","volume":9,"article_number":"224","type":"journal_article","abstract":[{"text":"Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer’s disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative).","lang":"eng"}],"extern":"1"},{"abstract":[{"lang":"eng","text":"There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations."}],"extern":"1","article_number":"1865","type":"journal_article","author":[{"first_name":"Jing","last_name":"Guo","full_name":"Guo, Jing"},{"full_name":"Wu, Yang","first_name":"Yang","last_name":"Wu"},{"full_name":"Zhu, Zhihong","last_name":"Zhu","first_name":"Zhihong"},{"last_name":"Zheng","first_name":"Zhili","full_name":"Zheng, Zhili"},{"full_name":"Trzaskowski, Maciej","last_name":"Trzaskowski","first_name":"Maciej"},{"first_name":"Jian","last_name":"Zeng","full_name":"Zeng, Jian"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"}],"date_updated":"2021-01-12T08:15:02Z","date_created":"2020-04-30T10:41:36Z","volume":9,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7713","year":"2018","publication_status":"published","title":"Global genetic differentiation of complex traits shaped by natural selection in humans","status":"public","intvolume":" 9","publisher":"Springer Nature","month":"05","day":"14","article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-018-04191-y","date_published":"2018-05-14T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nature Communications","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-04191-y"}],"citation":{"short":"J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson, P.M. Visscher, J. Yang, Nature Communications 9 (2018).","mla":"Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer Nature, 2018, doi:10.1038/s41467-018-04191-y.","chicago":"Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y.","ama":"Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y","ieee":"J. Guo et al., “Global genetic differentiation of complex traits shaped by natural selection in humans,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J. (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y","ista":"Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 9, 1865."},"article_type":"original","quality_controlled":"1"},{"extern":"1","year":"2018","publisher":"Cambridge University Press","publication_status":"published","author":[{"full_name":"Maier, R. M.","last_name":"Maier","first_name":"R. M."},{"first_name":"P. M.","last_name":"Visscher","full_name":"Visscher, P. M."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"last_name":"Wray","first_name":"N. R.","full_name":"Wray, N. R."}],"volume":48,"date_created":"2020-04-30T10:44:35Z","date_updated":"2021-01-12T08:15:05Z","publication_identifier":{"issn":["0033-2917","1469-8978"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/s0033291717002318"}],"oa":1,"quality_controlled":"1","doi":"10.1017/s0033291717002318","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","abstract":[{"text":"The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7721","intvolume":" 48","title":"Embracing polygenicity: A review of methods and tools for psychiatric genetics research","status":"public","oa_version":"Published Version","article_processing_charge":"No","day":"01","citation":{"ista":"Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 48(7), 1055–1067.","apa":"Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018). Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318","ieee":"R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity: A review of methods and tools for psychiatric genetics research,” Psychological Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.","ama":"Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 2018;48(7):1055-1067. doi:10.1017/s0033291717002318","chicago":"Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318.","mla":"Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no. 7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.","short":"R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine 48 (2018) 1055–1067."},"publication":"Psychological Medicine","page":"1055-1067","article_type":"original","date_published":"2018-05-01T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7723","year":"2018","publication_status":"published","title":"Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio","status":"public","publisher":"Genetics Society of America","intvolume":" 208","author":[{"first_name":"Luke R.","last_name":"Lloyd-Jones","full_name":"Lloyd-Jones, Luke R."},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."}],"date_updated":"2021-01-12T08:15:06Z","date_created":"2020-04-30T10:45:19Z","oa_version":"None","volume":208,"type":"journal_article","abstract":[{"text":"Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects.","lang":"eng"}],"issue":"4","extern":"1","publication":"Genetics","citation":{"chicago":"Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360.","mla":"Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360.","short":"L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408.","ista":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408.","apa":"Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360","ieee":"L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018.","ama":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360"},"quality_controlled":"1","article_type":"original","page":"1397-1408","date_published":"2018-04-01T00:00:00Z","doi":"10.1534/genetics.117.300360","language":[{"iso":"eng"}],"month":"04","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0016-6731","1943-2631"]}},{"language":[{"iso":"eng"}],"doi":"10.1038/s41588-018-0101-4","date_published":"2018-04-16T00:00:00Z","page":"746-753","quality_controlled":"1","article_type":"original","citation":{"chicago":"Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4.","short":"J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753.","mla":"Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4.","ieee":"J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018.","apa":"Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4","ista":"Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753.","ama":"Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4"},"publication":"Nature Genetics","article_processing_charge":"No","publication_identifier":{"issn":["1061-4036","1546-1718"]},"day":"16","month":"04","volume":50,"oa_version":"None","date_created":"2020-04-30T10:44:57Z","date_updated":"2021-01-12T08:15:06Z","author":[{"first_name":"Jian","last_name":"Zeng","full_name":"Zeng, Jian"},{"first_name":"Ronald","last_name":"de Vlaming","full_name":"de Vlaming, Ronald"},{"last_name":"Wu","first_name":"Yang","full_name":"Wu, Yang"},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Lloyd-Jones, Luke R.","first_name":"Luke R.","last_name":"Lloyd-Jones"},{"last_name":"Yengo","first_name":"Loic","full_name":"Yengo, Loic"},{"last_name":"Yap","first_name":"Chloe X.","full_name":"Yap, Chloe X."},{"last_name":"Xue","first_name":"Angli","full_name":"Xue, Angli"},{"last_name":"Sidorenko","first_name":"Julia","full_name":"Sidorenko, Julia"},{"full_name":"McRae, Allan F.","last_name":"McRae","first_name":"Allan F."},{"full_name":"Powell, Joseph E.","last_name":"Powell","first_name":"Joseph E."},{"full_name":"Montgomery, Grant W.","last_name":"Montgomery","first_name":"Grant W."},{"last_name":"Metspalu","first_name":"Andres","full_name":"Metspalu, Andres"},{"full_name":"Esko, Tonu","last_name":"Esko","first_name":"Tonu"},{"last_name":"Gibson","first_name":"Greg","full_name":"Gibson, Greg"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"}],"intvolume":" 50","publisher":"Springer Nature","status":"public","publication_status":"published","title":"Signatures of negative selection in the genetic architecture of human complex traits","_id":"7722","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"5","abstract":[{"text":"We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1073/pnas.1707227114","date_published":"2018-01-02T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114.","short":"J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156.","chicago":"Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114.","ama":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114","ista":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156.","ieee":"J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018.","apa":"Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114"},"publication":"Proceedings of the National Academy of Sciences","page":"151-156","article_type":"original","quality_controlled":"1","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424","1091-6490"]},"day":"02","month":"01","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.1806837115"}]},"author":[{"full_name":"Sanjak, Jaleal S.","first_name":"Jaleal S.","last_name":"Sanjak"},{"full_name":"Sidorenko, Julia","first_name":"Julia","last_name":"Sidorenko"},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"last_name":"Thornton","first_name":"Kevin R.","full_name":"Thornton, Kevin R."},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"volume":115,"oa_version":"None","date_created":"2020-04-30T10:45:43Z","date_updated":"2021-01-12T08:15:07Z","_id":"7724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","intvolume":" 115","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","title":"Evidence of directional and stabilizing selection in contemporary humans","status":"public","issue":"1","abstract":[{"lang":"eng","text":"Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species."}],"extern":"1","type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-06851-5","date_published":"2018-10-19T00:00:00Z","quality_controlled":"1","article_type":"original","publication":"Nature Communications","oa":1,"citation":{"ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5","ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5."},"main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-06851-5","open_access":"1"}],"month":"10","day":"19","article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"date_created":"2020-04-30T11:38:01Z","date_updated":"2021-01-12T08:15:18Z","oa_version":"Published Version","volume":9,"author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"full_name":"Brenner, Michael P.","first_name":"Michael P.","last_name":"Brenner"},{"full_name":"Ribbeck, Katharina","last_name":"Ribbeck","first_name":"Katharina"}],"status":"public","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","publication_status":"published","intvolume":" 9","publisher":"Springer Nature","year":"2018","_id":"7754","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex.","lang":"eng"}],"article_number":"4348","type":"journal_article"},{"month":"11","day":"09","article_processing_charge":"No","publication":"bioRxiv","citation":{"ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, .","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.","ieee":"R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018.","chicago":"Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018.","mla":"Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018.","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/466771 "}],"oa":1,"page":"49","date_published":"2018-11-09T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","abstract":[{"lang":"eng","text":"The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies."}],"extern":"1","_id":"7783","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","publication_status":"published","status":"public","publisher":"Cold Spring Harbor Laboratory","author":[{"full_name":"Bevers, Roel P.J.","last_name":"Bevers","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."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Auwerx","first_name":"Johan","full_name":"Auwerx, Johan"},{"last_name":"Hollis","first_name":"Brian","full_name":"Hollis, Brian"},{"full_name":"Deplancke, Bart","first_name":"Bart","last_name":"Deplancke"}],"date_updated":"2021-01-12T08:15:30Z","date_created":"2020-04-30T13:09:37Z","oa_version":"Preprint"},{"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"779"}]},"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"oa_version":"None","volume":4,"date_created":"2019-02-14T13:24:11Z","date_updated":"2023-02-23T13:17:54Z","_id":"6001","year":"2018","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","intvolume":" 4","publication_status":"published","status":"public","title":"ThreadScan: Automatic and scalable memory reclamation","issue":"4","abstract":[{"lang":"eng","text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"type":"journal_article","article_number":"18","date_published":"2018-09-01T00:00:00Z","doi":"10.1145/3201897","language":[{"iso":"eng"}],"citation":{"ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.","mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018)."},"publication":"ACM Transactions on Parallel Computing","quality_controlled":"1","publication_identifier":{"issn":["2329-4949"]},"month":"09","day":"01","scopus_import":1},{"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"file_date_updated":"2020-07-14T12:48:03Z","type":"conference","date_created":"2020-05-10T22:00:51Z","date_updated":"2023-02-23T13:18:41Z","oa_version":"Published Version","file":[{"checksum":"a4336c167978e81891970e4e4517a8c3","date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","file_id":"7894","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":308339,"access_level":"open_access","file_name":"2018_ICLR_Polino.pdf"}],"author":[{"full_name":"Polino, Antonio","last_name":"Polino","first_name":"Antonio"},{"first_name":"Razvan","last_name":"Pascanu","full_name":"Pascanu, Razvan"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"status":"public","publication_status":"published","ddc":["000"],"title":"Model compression via distillation and quantization","department":[{"_id":"DaAl"}],"_id":"7812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","day":"01","month":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"language":[{"iso":"eng"}],"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2018-05-03","location":"Vancouver, Canada","start_date":"2018-04-30"},"date_published":"2018-05-01T00:00:00Z","quality_controlled":"1","publication":"6th International Conference on Learning Representations","external_id":{"arxiv":["1802.05668"]},"oa":1,"citation":{"chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018."}},{"abstract":[{"text":"Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.","lang":"ger"}],"issue":"19","type":"journal_article","file":[{"relation":"main_file","file_id":"7988","checksum":"81506e0f7079e1e3591f3cd9f626bf67","date_created":"2020-06-19T11:58:06Z","date_updated":"2020-07-14T12:48:06Z","access_level":"open_access","file_name":"2018_AngChemieDT_Mahne.pdf","file_size":674789,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","status":"public","title":"Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff","ddc":["540"],"intvolume":" 130","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7983","day":"04","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-05-04T00:00:00Z","article_type":"original","page":"5627-5631","publication":"Angewandte Chemie","citation":{"ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631.","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277","ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277","chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277.","mla":"Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277.","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","file_date_updated":"2020-07-14T12:48:06Z","date_created":"2020-06-19T08:33:24Z","date_updated":"2021-01-12T08:16:21Z","volume":130,"author":[{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"last_name":"Renfrew","first_name":"Sara E.","full_name":"Renfrew, Sara E."},{"full_name":"McCloskey, Bryan D.","first_name":"Bryan D.","last_name":"McCloskey"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"}],"publication_status":"published","publisher":"Wiley","year":"2018","month":"05","publication_identifier":{"issn":["0044-8249"]},"language":[{"iso":"eng"}],"doi":"10.1002/ange.201802277","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1},{"month":"04","publication_identifier":{"issn":["0896-6273"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2018.03.028","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2018.03.028","open_access":"1"}],"external_id":{"pmid":["29621492"]},"extern":"1","date_updated":"2021-01-12T08:16:31Z","date_created":"2020-06-25T12:53:39Z","volume":98,"author":[{"first_name":"Jake P.","last_name":"Stroud","full_name":"Stroud, Jake P."},{"first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"publication_status":"published","publisher":"Elsevier","year":"2018","pmid":1,"day":"04","article_processing_charge":"No","date_published":"2018-04-04T00:00:00Z","article_type":"original","page":"8-9","publication":"Neuron","citation":{"ista":"Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.","apa":"Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028","ieee":"J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.","ama":"Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028","chicago":"Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.","mla":"Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.","short":"J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9."},"abstract":[{"lang":"eng","text":"The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. "}],"issue":"1","type":"journal_article","oa_version":"Published Version","status":"public","title":"Cortical signal propagation: Balance, amplify, transmit","intvolume":" 98","_id":"8015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"No","day":"01","citation":{"ama":"Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0","ieee":"J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.","apa":"Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0","ista":"Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783.","short":"J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783.","mla":"Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0.","chicago":"Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0."},"publication":"Nature Neuroscience","page":"1774-1783","article_type":"original","date_published":"2018-12-01T00:00:00Z","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity."}],"_id":"8073","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 21","status":"public","title":"Motor primitives in space and time via targeted gain modulation in cortical networks","oa_version":"Submitted Version","publication_identifier":{"issn":["1097-6256","1546-1726"]},"month":"12","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/","open_access":"1"}],"external_id":{"pmid":["30482949"]},"oa":1,"quality_controlled":"1","doi":"10.1038/s41593-018-0276-0","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2018","publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41593-018-0307-x"}]},"author":[{"full_name":"Stroud, Jake P.","first_name":"Jake P.","last_name":"Stroud"},{"full_name":"Porter, Mason A.","first_name":"Mason A.","last_name":"Porter"},{"full_name":"Hennequin, Guillaume","first_name":"Guillaume","last_name":"Hennequin"},{"full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"}],"volume":21,"date_updated":"2021-01-12T08:16:46Z","date_created":"2020-06-30T13:18:02Z"},{"type":"journal_article","issue":"3","extern":"1","_id":"8231","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","publication_status":"published","intvolume":" 142","publisher":"Elsevier","author":[{"full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"full_name":"Ilieva, Kristina M.","last_name":"Ilieva","first_name":"Kristina M."},{"full_name":"Matz, Miroslawa","first_name":"Miroslawa","last_name":"Matz"},{"full_name":"Herrmann, Ina","last_name":"Herrmann","first_name":"Ina"},{"full_name":"Spillner, Edzard","last_name":"Spillner","first_name":"Edzard"},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"date_updated":"2021-01-12T08:17:37Z","date_created":"2020-08-10T11:51:36Z","oa_version":"Published Version","volume":142,"day":"01","month":"09","article_processing_charge":"No","publication_identifier":{"issn":["0091-6749"]},"publication":"Journal of Allergy and Clinical Immunology","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.jaci.2018.04.021","open_access":"1"}],"citation":{"ista":"Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.","ieee":"J. Singer et al., “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","apa":"Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021","chicago":"Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.","mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.","short":"J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11."},"quality_controlled":"1","article_type":"letter_note","page":"973-976.e11","doi":"10.1016/j.jaci.2018.04.021","date_published":"2018-09-01T00:00:00Z","language":[{"iso":"eng"}]},{"article_processing_charge":"No","publication_identifier":{"issn":["1555-4309","1555-4317"]},"day":"13","month":"02","quality_controlled":"1","article_type":"original","citation":{"ista":"Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.","ieee":"T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.","apa":"Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830","ama":"Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830","chicago":"Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.","mla":"Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.","short":"T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018)."},"main_file_link":[{"url":"https://doi.org/10.1155/2018/1269830","open_access":"1"}],"oa":1,"publication":"Contrast Media & Molecular Imaging","language":[{"iso":"eng"}],"doi":"10.1155/2018/1269830","date_published":"2018-02-13T00:00:00Z","type":"journal_article","article_number":"1269830","extern":"1","abstract":[{"lang":"eng","text":"Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY."}],"publisher":"Hindawi","intvolume":" 2018","publication_status":"published","status":"public","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8234","year":"2018","volume":2018,"oa_version":"Published Version","date_updated":"2021-01-12T08:17:38Z","date_created":"2020-08-10T11:53:07Z","author":[{"full_name":"Balber, T.","first_name":"T.","last_name":"Balber"},{"full_name":"Singer, Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Singer","first_name":"Judit"},{"last_name":"Berroterán-Infante","first_name":"N.","full_name":"Berroterán-Infante, N."},{"full_name":"Dumanic, M.","last_name":"Dumanic","first_name":"M."},{"full_name":"Fetty, L.","last_name":"Fetty","first_name":"L."},{"full_name":"Fazekas-Singer, J.","first_name":"J.","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502"},{"first_name":"C.","last_name":"Vraka","full_name":"Vraka, C."},{"full_name":"Nics, L.","first_name":"L.","last_name":"Nics"},{"last_name":"Bergmann","first_name":"M.","full_name":"Bergmann, M."},{"last_name":"Pallitsch","first_name":"K.","full_name":"Pallitsch, K."},{"first_name":"H.","last_name":"Spreitzer","full_name":"Spreitzer, H."},{"full_name":"Wadsak, W.","first_name":"W.","last_name":"Wadsak","orcid":"0000-0003-4479-8053"},{"first_name":"M.","last_name":"Hacker","full_name":"Hacker, M."},{"last_name":"Jensen-Jarolim","first_name":"E.","full_name":"Jensen-Jarolim, E."},{"full_name":"Viernstein, H.","last_name":"Viernstein","first_name":"H."},{"full_name":"Mitterhauser, M.","orcid":"0000-0003-3173-5272","last_name":"Mitterhauser","first_name":"M."}]},{"publication":"Oncotarget","oa":1,"citation":{"short":"T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038.","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.","chicago":"Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876.","ama":"Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876","apa":"Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876","ieee":"T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018.","ista":"Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038."},"main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.24876","open_access":"1"}],"quality_controlled":"1","article_type":"original","page":"19026-19038","date_published":"2018-04-10T00:00:00Z","doi":"10.18632/oncotarget.24876","language":[{"iso":"eng"}],"month":"04","day":"10","publication_identifier":{"eissn":["1949-2553"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8232","year":"2018","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","publication_status":"published","status":"public","publisher":"Impact Journals","intvolume":" 9","author":[{"last_name":"Nagaya","first_name":"Tadanobu","full_name":"Nagaya, Tadanobu"},{"full_name":"Okuyama, Shuhei","last_name":"Okuyama","first_name":"Shuhei"},{"full_name":"Ogata, Fusa","last_name":"Ogata","first_name":"Fusa"},{"full_name":"Maruoka, Yasuhiro","last_name":"Maruoka","first_name":"Yasuhiro"},{"first_name":"Deborah W.","last_name":"Knapp","full_name":"Knapp, Deborah W."},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"first_name":"Peter L.","last_name":"Choyke","full_name":"Choyke, Peter L."},{"first_name":"Amy K.","last_name":"LeBlanc","full_name":"LeBlanc, Amy K."},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"full_name":"Kobayashi, Hisataka","first_name":"Hisataka","last_name":"Kobayashi"}],"date_created":"2020-08-10T11:52:54Z","date_updated":"2021-01-12T08:17:37Z","oa_version":"Published Version","volume":9,"type":"journal_article","abstract":[{"lang":"eng","text":"Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans."}],"extern":"1"},{"day":"01","article_processing_charge":"No","date_published":"2018-05-01T00:00:00Z","article_type":"original","page":"118-127","publication":"Developmental & Comparative Immunology","citation":{"ieee":"I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005","ista":"Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127.","ama":"Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005","chicago":"Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005.","short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005."},"abstract":[{"text":"The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Published Version","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","status":"public","intvolume":" 82","_id":"8233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"issn":["0145-305X"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.dci.2018.01.005","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.dci.2018.01.005","open_access":"1"}],"extern":"1","date_created":"2020-08-10T11:53:01Z","date_updated":"2021-01-12T08:17:38Z","volume":82,"author":[{"first_name":"Ina","last_name":"Herrmann","full_name":"Herrmann, Ina"},{"first_name":"Jelena","last_name":"Gotovina","full_name":"Gotovina, Jelena"},{"first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"first_name":"Michael B.","last_name":"Fischer","full_name":"Fischer, Michael B."},{"full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"full_name":"Bianchini, Rodolfo","first_name":"Rodolfo","last_name":"Bianchini"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"publication_status":"published","publisher":"Elsevier","year":"2018"},{"status":"public","publication_status":"published","title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","publisher":"Springer Nature","intvolume":" 19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8262","year":"2018","date_updated":"2023-02-23T13:28:52Z","date_created":"2020-08-15T11:02:08Z","volume":19,"oa_version":"Published Version","author":[{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"full_name":"Moroz, Elena V.","last_name":"Moroz","first_name":"Elena V."},{"full_name":"Davydov, Iakov I.","first_name":"Iakov I.","last_name":"Davydov"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"article_number":"965","type":"journal_article","extern":"1","abstract":[{"text":"Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.","lang":"eng"}],"article_type":"original","quality_controlled":"1","publication":"BMC Genomics","citation":{"short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature, 2018, doi:10.1186/s12864-018-5245-1.","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1.","ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics, vol. 19. Springer Nature, 2018.","ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965."},"main_file_link":[{"url":"https://doi.org/10.1186/s12864-018-5245-1","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5245-1","date_published":"2018-12-27T00:00:00Z","day":"27","month":"12","publication_identifier":{"issn":["1471-2164"]},"article_processing_charge":"No"},{"doi":"10.7717/peerj.4545","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"external_id":{"pmid":["29607260"]},"quality_controlled":"1","month":"03","publication_identifier":{"issn":["2167-8359"]},"author":[{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Dranenko, Natalia O.","first_name":"Natalia O.","last_name":"Dranenko"},{"full_name":"Ocheredko, Elena S.","first_name":"Elena S.","last_name":"Ocheredko"},{"full_name":"Kanevsky, German M.","first_name":"German M.","last_name":"Kanevsky"},{"first_name":"Yaroslav N.","last_name":"Lozinsky","full_name":"Lozinsky, Yaroslav N."},{"full_name":"Khalaycheva, Vera A.","last_name":"Khalaycheva","first_name":"Vera A."},{"first_name":"Irena I.","last_name":"Artamonova","full_name":"Artamonova, Irena I."},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"date_created":"2020-08-15T11:08:23Z","date_updated":"2023-02-23T13:28:57Z","volume":6,"year":"2018","pmid":1,"publication_status":"published","publisher":"PeerJ","extern":"1","article_number":"e4545","date_published":"2018-03-27T00:00:00Z","publication":"PeerJ","citation":{"ieee":"O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.","apa":"Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545","ista":"Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545.","ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545","chicago":"Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.","short":"O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545."},"article_type":"original","day":"27","article_processing_charge":"No","oa_version":"Published Version","_id":"8265","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","status":"public","intvolume":" 6","abstract":[{"lang":"eng","text":"Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content."}],"type":"journal_article"},{"article_type":"original","quality_controlled":"1","page":"2811-2817","publication":"Anticancer Research","citation":{"chicago":"Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research. International Institute of Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525.","mla":"Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no. 5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525.","short":"M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G. Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38 (2018) 2811–2817.","ista":"Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG, Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.","apa":"Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer, J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. International Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525","ieee":"M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression between cancer cells and macrophages,” Anticancer Research, vol. 38, no. 5. International Institute of Anticancer Research, pp. 2811–2817, 2018.","ama":"Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817. doi:10.21873/anticanres.12525"},"language":[{"iso":"eng"}],"doi":"10.21873/anticanres.12525","date_published":"2018-05-01T00:00:00Z","month":"05","day":"01","publication_identifier":{"issn":["0250-7005"],"eissn":["1791-7530"]},"article_processing_charge":"No","title":"Bidirectional regulation of COX-2 expression between cancer cells and macrophages","publication_status":"published","status":"public","publisher":"International Institute of Anticancer Research","intvolume":" 38","year":"2018","_id":"8274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-17T07:13:55Z","date_updated":"2021-01-12T08:17:52Z","volume":38,"oa_version":"None","author":[{"full_name":"Carvalho, Maria Isabel","last_name":"Carvalho","first_name":"Maria Isabel"},{"full_name":"Bianchini, Rodolfo","first_name":"Rodolfo","last_name":"Bianchini"},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"full_name":"Flickinger, Irene","first_name":"Irene","last_name":"Flickinger"},{"first_name":"Johann G.","last_name":"Thalhammer","full_name":"Thalhammer, Johann G."},{"first_name":"Isabel","last_name":"Pires","full_name":"Pires, Isabel"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"last_name":"Queiroga","first_name":"Felisbina L.","full_name":"Queiroga, Felisbina L."}],"type":"journal_article","extern":"1","abstract":[{"text":"Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT.","lang":"eng"}],"issue":"5"},{"article_processing_charge":"No","publication_identifier":{"eisbn":["9783319990736"],"issn":["0302-9743","1611-3349"],"isbn":["9783319990729"]},"day":"08","month":"08","citation":{"ista":"Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS: European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.","ieee":"E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal scaling and confidentiality on permissioned blockchains,” in Computer Security, Barcelona, Spain, 2018, vol. 11098, pp. 111–131.","apa":"Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018). Channels: Horizontal scaling and confidentiality on permissioned blockchains. In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer Nature. https://doi.org/10.1007/978-3-319-99073-6_6","ama":"Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal scaling and confidentiality on permissioned blockchains. In: Computer Security. Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6","chicago":"Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.","mla":"Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature, 2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.","short":"E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security, Springer Nature, 2018, pp. 111–131."},"publication":"Computer Security","page":"111-131","quality_controlled":"1","date_published":"2018-08-08T00:00:00Z","doi":"10.1007/978-3-319-99073-6_6","conference":{"end_date":"2018-09-07","location":"Barcelona, Spain","start_date":"2018-09-03","name":"ESORICS: European Symposium on Research in Computer Security"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Sharding, or partitioning the system’s state so that different subsets of participants handle it, is a proven approach to building distributed systems whose total capacity scales horizontally with the number of participants. Many distributed ledgers have adopted this approach to increase their performance, however, they focus on the permissionless setting that assumes the existence of a strong adversary. In this paper, we deploy channels for permissioned blockchains. Our first contribution is to adapt sharding on asset-management applications for the permissioned setting, while preserving liveness and safety even on transactions spanning across-channels. Our second contribution is to leverage channels as a confidentiality boundary, enabling different organizations and consortia to preserve their privacy within their channels and still be part of a bigger collaborative ecosystem. To make our system concrete we map it on top of Hyperledger Fabric."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8298","year":"2018","publisher":"Springer Nature","intvolume":" 11098","status":"public","title":"Channels: Horizontal scaling and confidentiality on permissioned blockchains","publication_status":"published","author":[{"last_name":"Androulaki","first_name":"Elli","full_name":"Androulaki, Elli"},{"full_name":"Cachin, Christian","first_name":"Christian","last_name":"Cachin"},{"full_name":"De Caro, Angelo","first_name":"Angelo","last_name":"De Caro"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"}],"oa_version":"None","volume":11098,"date_created":"2020-08-26T11:47:34Z","date_updated":"2021-01-12T08:17:57Z"},{"type":"conference","abstract":[{"lang":"eng","text":"Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm 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 crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds."}],"extern":"1","_id":"8297","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"IEEE","status":"public","publication_status":"published","title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"first_name":"Linus","last_name":"Gasser","full_name":"Gasser, Linus"},{"first_name":"Nicolas","last_name":"Gailly","full_name":"Gailly, Nicolas"},{"full_name":"Syta, Ewa","first_name":"Ewa","last_name":"Syta"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"oa_version":"Preprint","date_created":"2020-08-26T11:46:35Z","date_updated":"2021-01-12T08:17:56Z","article_processing_charge":"No","publication_identifier":{"issn":["2375-1207"],"isbn":["9781538643532"]},"day":"26","month":"07","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/406"}],"oa":1,"citation":{"short":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.","mla":"Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–98, doi:10.1109/sp.2018.000-5.","chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98. IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.","ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., & Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5","ieee":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2018, pp. 583–598.","ista":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598."},"publication":"2018 IEEE Symposium on Security and Privacy","page":"583-598","quality_controlled":"1","doi":"10.1109/sp.2018.000-5","date_published":"2018-07-26T00:00:00Z","conference":{"location":"San Francisco, CA, United States","start_date":"2018-05-20","end_date":"2018-05-24","name":"SP: Symposium on Security and Privacy"},"language":[{"iso":"eng"}]},{"keyword":["General Materials Science"],"day":"03","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["1948-7185"]},"publication":"The Journal of Physical Chemistry Letters","citation":{"mla":"Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38, doi:10.1021/acs.jpclett.8b00269.","short":"V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher, M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez, B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.","chicago":"Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpclett.8b00269.","ama":"Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269","ista":"Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 9(5), 933–938.","ieee":"V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938, 2018.","apa":"Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L., … Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269"},"quality_controlled":"1","article_type":"original","page":"933-938","date_published":"2018-02-03T00:00:00Z","doi":"10.1021/acs.jpclett.8b00269","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states.","lang":"eng"}],"issue":"5","extern":"1","_id":"8443","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine","status":"public","publication_status":"published","publisher":"American Chemical Society","intvolume":" 9","author":[{"last_name":"Kurauskas","first_name":"Vilius","full_name":"Kurauskas, Vilius"},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"last_name":"Lunetti","first_name":"Paola","full_name":"Lunetti, Paola"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"last_name":"Imbert","first_name":"Lionel","full_name":"Imbert, Lionel"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"full_name":"King, Martin S.","first_name":"Martin S.","last_name":"King"},{"full_name":"Sounier, Rémy","first_name":"Rémy","last_name":"Sounier"},{"full_name":"Dolce, Vincenza","first_name":"Vincenza","last_name":"Dolce"},{"last_name":"Kunji","first_name":"Edmund R. S.","full_name":"Kunji, Edmund R. S."},{"full_name":"Capobianco, Loredana","last_name":"Capobianco","first_name":"Loredana"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"date_created":"2020-09-18T10:05:45Z","date_updated":"2021-01-12T08:19:18Z","volume":9,"oa_version":"None"},{"author":[{"full_name":"Weinhäupl, Katharina","first_name":"Katharina","last_name":"Weinhäupl"},{"first_name":"Martha","last_name":"Brennich","full_name":"Brennich, Martha"},{"first_name":"Uli","last_name":"Kazmaier","full_name":"Kazmaier, Uli"},{"full_name":"Lelievre, Joel","first_name":"Joel","last_name":"Lelievre"},{"first_name":"Lluis","last_name":"Ballell","full_name":"Ballell, Lluis"},{"first_name":"Alfred","last_name":"Goldberg","full_name":"Goldberg, Alfred"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Fraga, Hugo","first_name":"Hugo","last_name":"Fraga"}],"date_created":"2020-09-18T10:05:18Z","date_updated":"2021-01-12T08:19:17Z","oa_version":"None","volume":293,"_id":"8440","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","title":"The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis","status":"public","intvolume":" 293","publisher":"American Society for Biochemistry & Molecular Biology","abstract":[{"text":"Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death.","lang":"eng"}],"issue":"22","extern":"1","type":"journal_article","date_published":"2018-06-01T00:00:00Z","doi":"10.1074/jbc.ra118.002251","language":[{"iso":"eng"}],"publication":"Journal of Biological Chemistry","citation":{"apa":"Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg, A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251","ieee":"K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,” Journal of Biological Chemistry, vol. 293, no. 22. American Society for Biochemistry & Molecular Biology, pp. 8379–8393, 2018.","ista":"Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 293(22), 8379–8393.","ama":"Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393. doi:10.1074/jbc.ra118.002251","chicago":"Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251.","short":"K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg, P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393.","mla":"Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry, vol. 293, no. 22, American Society for Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251."},"article_type":"original","quality_controlled":"1","page":"8379-8393","day":"01","month":"06","article_processing_charge":"No","publication_identifier":{"issn":["0021-9258","1083-351X"]},"keyword":["Cell Biology","Biochemistry","Molecular Biology"]},{"language":[{"iso":"eng"}],"date_published":"2018-02-28T00:00:00Z","doi":"10.1021/acs.chemrev.7b00570","article_type":"original","quality_controlled":"1","page":"3559-3607","publication":"Chemical Reviews","citation":{"mla":"Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society, 2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.","short":"C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire, B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118 (2018) 3559–3607.","chicago":"Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews. American Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.","ama":"Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570","ista":"Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.","apa":"Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570","ieee":"C. Chipot et al., “Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society, pp. 3559–3607, 2018."},"day":"28","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["0009-2665","1520-6890"]},"keyword":["General Chemistry"],"date_updated":"2021-01-12T08:19:18Z","date_created":"2020-09-18T10:05:35Z","volume":118,"oa_version":"None","author":[{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"first_name":"Jason R.","last_name":"Schnell","full_name":"Schnell, Jason R."},{"last_name":"Zitzmann","first_name":"Nicole","full_name":"Zitzmann, Nicole"},{"last_name":"Pebay-Peyroula","first_name":"Eva","full_name":"Pebay-Peyroula, Eva"},{"full_name":"Catoire, Laurent J.","last_name":"Catoire","first_name":"Laurent J."},{"first_name":"Bruno","last_name":"Miroux","full_name":"Miroux, Bruno"},{"first_name":"Edmund R. S.","last_name":"Kunji","full_name":"Kunji, Edmund R. S."},{"last_name":"Veglia","first_name":"Gianluigi","full_name":"Veglia, Gianluigi"},{"full_name":"Cross, Timothy A.","last_name":"Cross","first_name":"Timothy A."},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"title":"Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies","status":"public","publication_status":"published","publisher":"American Chemical Society","intvolume":" 118","_id":"8442","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","extern":"1","abstract":[{"text":"Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.","lang":"eng"}],"issue":"7","type":"journal_article"},{"extern":"1","issue":"1","abstract":[{"text":"Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process.","lang":"eng"}],"type":"journal_article","volume":71,"oa_version":"Published Version","date_created":"2020-09-18T10:05:28Z","date_updated":"2021-01-12T08:19:17Z","author":[{"full_name":"Krushelnitsky, Alexey","last_name":"Krushelnitsky","first_name":"Alexey"},{"last_name":"Gauto","first_name":"Diego","full_name":"Gauto, Diego"},{"full_name":"Rodriguez Camargo, Diana C.","last_name":"Rodriguez Camargo","first_name":"Diana C."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"full_name":"Saalwächter, Kay","first_name":"Kay","last_name":"Saalwächter"}],"intvolume":" 71","publisher":"Springer Nature","title":"Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals","status":"public","publication_status":"published","year":"2018","_id":"8441","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0925-2738","1573-5001"]},"article_processing_charge":"No","day":"30","month":"05","language":[{"iso":"eng"}],"date_published":"2018-05-30T00:00:00Z","doi":"10.1007/s10858-018-0191-4","page":"53-67","article_type":"original","quality_controlled":"1","citation":{"chicago":"Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda, and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.","mla":"Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp. 53–67, doi:10.1007/s10858-018-0191-4.","short":"A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter, Journal of Biomolecular NMR 71 (2018) 53–67.","ista":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. 2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 71(1), 53–67.","apa":"Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., & Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4","ieee":"A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter, “Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals,” Journal of Biomolecular NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.","ama":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4"},"publication":"Journal of Biomolecular NMR"},{"date_published":"2018-07-02T00:00:00Z","doi":"10.1021/acschembio.8b00271","language":[{"iso":"eng"}],"publication":"ACS Chemical Biology","citation":{"mla":"Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society, 2018, pp. 2106–13, doi:10.1021/acschembio.8b00271.","short":"C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi, A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.","chicago":"Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology. American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271.","ama":"Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113. doi:10.1021/acschembio.8b00271","ista":"Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 13(8), 2106–2113.","ieee":"C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society, pp. 2106–2113, 2018.","apa":"Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi, A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271"},"article_type":"original","quality_controlled":"1","page":"2106-2113","month":"07","day":"02","article_processing_charge":"No","publication_identifier":{"issn":["1554-8929","1554-8937"]},"keyword":["Molecular Medicine","Biochemistry","General Medicine"],"author":[{"full_name":"Laguri, Cedric","last_name":"Laguri","first_name":"Cedric"},{"first_name":"Alba","last_name":"Silipo","full_name":"Silipo, Alba"},{"full_name":"Martorana, Alessandra M.","first_name":"Alessandra M.","last_name":"Martorana"},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Marchetti, Roberta","first_name":"Roberta","last_name":"Marchetti"},{"full_name":"Polissi, Alessandra","last_name":"Polissi","first_name":"Alessandra"},{"full_name":"Molinaro, Antonio","first_name":"Antonio","last_name":"Molinaro"},{"full_name":"Simorre, Jean-Pierre","last_name":"Simorre","first_name":"Jean-Pierre"}],"date_updated":"2021-01-12T08:19:16Z","date_created":"2020-09-18T10:05:09Z","volume":13,"oa_version":"None","_id":"8439","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Solid state NMR studies of intact lipopolysaccharide endotoxin","intvolume":" 13","publisher":"American Chemical Society","abstract":[{"lang":"eng","text":"Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria."}],"issue":"8","extern":"1","type":"journal_article"},{"day":"13","month":"12","article_processing_charge":"No","publication":"bioRxiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088"},"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"}],"date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","language":[{"iso":"eng"}],"type":"preprint","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"ec_funded":1,"_id":"8547","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","publication_status":"submitted","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"SiHi"}],"author":[{"last_name":"Llorca","first_name":"Alfredo","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"first_name":"Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"last_name":"Wong","first_name":"Fong K.","full_name":"Wong, Fong K."},{"full_name":"Diana, Giovanni","last_name":"Diana","first_name":"Giovanni"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"last_name":"Meyer","first_name":"Martin","full_name":"Meyer, Martin"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Maravall, Miguel","first_name":"Miguel","last_name":"Maravall"},{"full_name":"Marín, Oscar","last_name":"Marín","first_name":"Oscar"}],"date_created":"2020-09-21T12:01:50Z","date_updated":"2021-01-12T08:20:00Z","oa_version":"Preprint"},{"abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"type":"book_chapter","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:48:14Z","date_created":"2019-11-19T08:22:18Z","checksum":"9995c6ce6957333baf616fc4f20be597","relation":"main_file","file_id":"7053","content_type":"application/pdf","file_size":516307,"creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","access_level":"open_access"}],"_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10760","ddc":["000"],"status":"public","title":"Computing average response time","has_accepted_license":"1","day":"20","scopus_import":1,"date_published":"2018-07-20T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9"},"publication":"Principles of Modeling","page":"143 - 161","ec_funded":1,"publist_id":"7968","file_date_updated":"2020-07-14T12:48:14Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"volume":10760,"date_updated":"2021-01-12T08:20:14Z","date_created":"2018-12-11T11:44:33Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","year":"2018","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","editor":[{"last_name":"Lohstroh","first_name":"Marten","full_name":"Lohstroh, Marten"},{"full_name":"Derler, Patricia","last_name":"Derler","first_name":"Patricia"},{"last_name":"Sirjani","first_name":"Marjan","full_name":"Sirjani, Marjan"}],"publication_status":"published","month":"07","doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” Nature Physics, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018.","apa":"Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0227-4","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:10.1038/s41567-018-0227-4.","chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4."},"publication":"Nature Physics","page":"1114-1118","article_type":"original","date_published":"2018-11-01T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery.","lang":"eng"}],"_id":"9062","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 14","title":"Targeted assembly and synchronization of self-spinning microgears","status":"public","oa_version":"Preprint","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"11","oa":1,"external_id":{"arxiv":["1810.01033"]},"main_file_link":[{"url":"https://arxiv.org/abs/1810.01033","open_access":"1"}],"quality_controlled":"1","doi":"10.1038/s41567-018-0227-4","language":[{"iso":"eng"}],"extern":"1","year":"2018","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"last_name":"Youssef","first_name":"Mena","full_name":"Youssef, Mena"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"}],"volume":14,"date_updated":"2023-02-23T13:48:02Z","date_created":"2021-02-02T13:52:49Z"},{"page":"11","article_type":"letter_note","citation":{"mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018."},"publication":"Opera Medica et Physiologica","date_published":"2018-06-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"30","intvolume":" 4","title":"Diffraction-unlimited optical imaging for synaptic physiology","status":"public","_id":"9229","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","alternative_title":["Molecular and cellular neuroscience"],"type":"journal_article","issue":"S1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"language":[{"iso":"eng"}],"doi":"10.20388/omp2018.00s1.001","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"month":"06","publisher":"Lobachevsky State University of Nizhny Novgorod","department":[{"_id":"JoDa"}],"publication_status":"published","year":"2018","volume":4,"date_updated":"2021-12-03T07:31:05Z","date_created":"2021-03-07T23:01:25Z","author":[{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}]},{"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:15Z","article_number":"23","date_created":"2019-02-14T14:12:09Z","date_updated":"2023-02-23T14:02:58Z","volume":117,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"963"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2018","month":"08","publication_identifier":{"issn":["1868-8969"]},"language":[{"iso":"eng"}],"conference":{"location":"Liverpool, United Kingdom","start_date":"2018-08-27","end_date":"2018-08-31","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.4230/LIPICS.MFCS.2018.23","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"6007","relation":"main_file","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","access_level":"open_access","file_name":"2018_LIPIcs_Avni.pdf","creator":"dernst","content_type":"application/pdf","file_size":542889}],"status":"public","ddc":["000"],"title":"Timed network games with clocks","intvolume":" 117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6005","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","citation":{"short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23."}},{"extern":"1","volume":20,"date_updated":"2021-08-09T12:36:47Z","date_created":"2021-07-15T12:51:44Z","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"Christoph","last_name":"Dellago","full_name":"Dellago, Christoph"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"publisher":"Royal Society of Chemistry","publication_status":"published","pmid":1,"year":"2018","publication_identifier":{"issn":["1463-9076"],"eissn":["1463-9084"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1039/c8cp04561e","quality_controlled":"1","external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05551"}],"oa":1,"issue":"45","abstract":[{"lang":"eng","text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 20","status":"public","title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9668","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2018-12-07T00:00:00Z","page":"28732-28740","article_type":"original","citation":{"ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018.","apa":"Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e","ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e","chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c8cp04561e.","short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740.","mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:10.1039/c8cp04561e."},"publication":"Physical Chemistry Chemical Physics"},{"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"volume":97,"date_updated":"2021-08-09T12:38:26Z","date_created":"2021-07-19T09:39:48Z","year":"2018","publisher":"American Physical Society","publication_status":"published","extern":"1","article_number":"054102","doi":"10.1103/physrevb.97.054102","language":[{"iso":"eng"}],"external_id":{"arxiv":["1710.02815"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02815"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"02","oa_version":"Preprint","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9687","intvolume":" 97","status":"public","title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","issue":"5","abstract":[{"lang":"eng","text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures."}],"type":"journal_article","date_published":"2018-02-01T00:00:00Z","citation":{"ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","apa":"Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” Physical Review B, vol. 97, no. 5. American Physical Society, 2018.","ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 2018;97(5). doi:10.1103/physrevb.97.054102","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018)."},"publication":"Physical Review B","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"article_number":"e2005372","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","year":"2018","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}],"volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","publication_identifier":{"issn":["15449173"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","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."}],"_id":"315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"status":"public","oa_version":"Published Version","file":[{"file_id":"5870","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","creator":"dernst","file_size":6968201,"content_type":"application/pdf"}],"scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372"},"publication":"PLoS Biology","date_published":"2018-06-15T00:00:00Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The restricted planar elliptic three body problem (RPETBP) describes the motion of a massless particle (a comet or an asteroid) under the gravitational field of two massive bodies (the primaries, say the Sun and Jupiter) revolving around their center of mass on elliptic orbits with some positive eccentricity. The aim of this paper is to show the existence of orbits whose angular momentum performs arbitrary excursions in a large region. In particular, there exist diffusive orbits, that is, with a large variation of angular momentum. The leading idea of the proof consists in analyzing parabolic motions of the comet. By a well-known result of McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable (resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold at parabolic infinity. On P∞ it is possible to define two scattering maps, which contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic both in the future and the past. Since the inner dynamics inside P∞ is trivial, two different scattering maps are used. The combination of these two scattering maps permits the design of the desired diffusive pseudo-orbits. Using shadowing techniques and these pseudo orbits we show the existence of true trajectories of the RPETBP whose angular momentum varies in any predetermined fashion."}],"issue":"3","extern":"1","_id":"8417","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Global instability in the restricted planar elliptic three body problem","publication_status":"published","intvolume":" 366","publisher":"Springer Nature","author":[{"last_name":"Delshams","first_name":"Amadeu","full_name":"Delshams, Amadeu"},{"full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"full_name":"de la Rosa, Abraham","first_name":"Abraham","last_name":"de la Rosa"},{"first_name":"Tere M.","last_name":"Seara","full_name":"Seara, Tere M."}],"date_created":"2020-09-17T10:41:43Z","date_updated":"2021-01-12T08:19:08Z","volume":366,"oa_version":"None","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"month":"09","day":"05","publication_identifier":{"issn":["0010-3616","1432-0916"]},"article_processing_charge":"No","publication":"Communications in Mathematical Physics","citation":{"ama":"Delshams A, Kaloshin V, de la Rosa A, Seara TM. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 2018;366(3):1173-1228. doi:10.1007/s00220-018-3248-z","ista":"Delshams A, Kaloshin V, de la Rosa A, Seara TM. 2018. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 366(3), 1173–1228.","ieee":"A. Delshams, V. Kaloshin, A. de la Rosa, and T. M. Seara, “Global instability in the restricted planar elliptic three body problem,” Communications in Mathematical Physics, vol. 366, no. 3. Springer Nature, pp. 1173–1228, 2018.","apa":"Delshams, A., Kaloshin, V., de la Rosa, A., & Seara, T. M. (2018). Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-018-3248-z","mla":"Delshams, Amadeu, et al. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics, vol. 366, no. 3, Springer Nature, 2018, pp. 1173–228, doi:10.1007/s00220-018-3248-z.","short":"A. Delshams, V. Kaloshin, A. de la Rosa, T.M. Seara, Communications in Mathematical Physics 366 (2018) 1173–1228.","chicago":"Delshams, Amadeu, Vadim Kaloshin, Abraham de la Rosa, and Tere M. Seara. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics. Springer Nature, 2018. https://doi.org/10.1007/s00220-018-3248-z."},"article_type":"original","quality_controlled":"1","page":"1173-1228","doi":"10.1007/s00220-018-3248-z","date_published":"2018-09-05T00:00:00Z","language":[{"iso":"eng"}]},{"extern":"1","date_updated":"2021-01-12T08:19:11Z","date_created":"2020-09-17T10:42:30Z","volume":28,"author":[{"last_name":"Huang","first_name":"Guan","full_name":"Huang, Guan"},{"full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"full_name":"Sorrentino, Alfonso","first_name":"Alfonso","last_name":"Sorrentino"}],"publication_status":"published","publisher":"Springer Nature","year":"2018","month":"03","publication_identifier":{"issn":["1016-443X","1420-8970"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00039-018-0440-4","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.10601"}],"oa":1,"external_id":{"arxiv":["1705.10601"]},"abstract":[{"text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Preprint","status":"public","title":"Nearly circular domains which are integrable close to the boundary are ellipses","intvolume":" 28","_id":"8422","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"18","article_processing_charge":"No","keyword":["Geometry and Topology","Analysis"],"date_published":"2018-03-18T00:00:00Z","article_type":"original","page":"334-392","publication":"Geometric and Functional Analysis","citation":{"chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4.","mla":"Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.","short":"G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28 (2018) 334–392.","ista":"Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 28(2), 334–392.","apa":"Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” Geometric and Functional Analysis, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.","ama":"Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 2018;28(2):334-392. doi:10.1007/s00039-018-0440-4"}},{"extern":"1","year":"2018","publisher":"Annals of Mathematics, Princeton U","publication_status":"published","author":[{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"last_name":"Sorrentino","first_name":"Alfonso","full_name":"Sorrentino, Alfonso"}],"volume":188,"date_created":"2020-09-17T10:42:22Z","date_updated":"2021-01-12T08:19:10Z","publication_identifier":{"issn":["0003-486X"]},"month":"07","oa":1,"external_id":{"arxiv":["1612.09194"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.09194"}],"quality_controlled":"1","doi":"10.4007/annals.2018.188.1.6","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"text":"The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains.","lang":"eng"}],"_id":"8421","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 188","status":"public","title":"On the local Birkhoff conjecture for convex billiards","oa_version":"Preprint","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"article_processing_charge":"No","day":"01","citation":{"short":"V. Kaloshin, A. Sorrentino, Annals of Mathematics 188 (2018) 315–380.","mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics, vol. 188, no. 1, Annals of Mathematics, Princeton U, 2018, pp. 315–80, doi:10.4007/annals.2018.188.1.6.","chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics. Annals of Mathematics, Princeton U, 2018. https://doi.org/10.4007/annals.2018.188.1.6.","ama":"Kaloshin V, Sorrentino A. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 2018;188(1):315-380. doi:10.4007/annals.2018.188.1.6","ieee":"V. Kaloshin and A. Sorrentino, “On the local Birkhoff conjecture for convex billiards,” Annals of Mathematics, vol. 188, no. 1. Annals of Mathematics, Princeton U, pp. 315–380, 2018.","apa":"Kaloshin, V., & Sorrentino, A. (2018). On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. Annals of Mathematics, Princeton U. https://doi.org/10.4007/annals.2018.188.1.6","ista":"Kaloshin V, Sorrentino A. 2018. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 188(1), 315–380."},"publication":"Annals of Mathematics","page":"315-380","article_type":"original","date_published":"2018-07-01T00:00:00Z"},{"month":"10","day":"28","article_processing_charge":"No","publication_identifier":{"issn":["1364-503X","1471-2962"]},"keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"language":[{"iso":"eng"}],"doi":"10.1098/rsta.2017.0419","date_published":"2018-10-28T00:00:00Z","quality_controlled":"1","article_type":"original","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"ama":"Kaloshin V, Sorrentino A. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2018;376(2131). doi:10.1098/rsta.2017.0419","ista":"Kaloshin V, Sorrentino A. 2018. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 376(2131), 20170419.","apa":"Kaloshin, V., & Sorrentino, A. (2018). On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2017.0419","ieee":"V. Kaloshin and A. Sorrentino, “On the integrability of Birkhoff billiards,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131. The Royal Society, 2018.","mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131, 20170419, The Royal Society, 2018, doi:10.1098/rsta.2017.0419.","short":"V. Kaloshin, A. Sorrentino, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 376 (2018).","chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2018. https://doi.org/10.1098/rsta.2017.0419."},"extern":"1","abstract":[{"text":"In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture.\r\n\r\nThis article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.","lang":"eng"}],"issue":"2131","article_number":"20170419","type":"journal_article","date_created":"2020-09-17T10:42:01Z","date_updated":"2021-01-12T08:19:09Z","volume":376,"oa_version":"None","author":[{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Sorrentino, Alfonso","last_name":"Sorrentino","first_name":"Alfonso"}],"publication_status":"published","status":"public","title":"On the integrability of Birkhoff billiards","intvolume":" 376","publisher":"The Royal Society","_id":"8419","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018"},{"day":"15","article_processing_charge":"No","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"date_published":"2018-10-15T00:00:00Z","publication":"Nonlinearity","citation":{"short":"V. Kaloshin, K. Zhang, Nonlinearity 31 (2018) 5214–5234.","mla":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity, vol. 31, no. 11, IOP Publishing, 2018, pp. 5214–34, doi:10.1088/1361-6544/aadc12.","chicago":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity. IOP Publishing, 2018. https://doi.org/10.1088/1361-6544/aadc12.","ama":"Kaloshin V, Zhang K. Density of convex billiards with rational caustics. Nonlinearity. 2018;31(11):5214-5234. doi:10.1088/1361-6544/aadc12","ieee":"V. Kaloshin and K. Zhang, “Density of convex billiards with rational caustics,” Nonlinearity, vol. 31, no. 11. IOP Publishing, pp. 5214–5234, 2018.","apa":"Kaloshin, V., & Zhang, K. (2018). Density of convex billiards with rational caustics. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/aadc12","ista":"Kaloshin V, Zhang K. 2018. Density of convex billiards with rational caustics. Nonlinearity. 31(11), 5214–5234."},"article_type":"original","page":"5214-5234","abstract":[{"lang":"eng","text":"We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case."}],"issue":"11","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8420","status":"public","title":"Density of convex billiards with rational caustics","intvolume":" 31","month":"10","publication_identifier":{"issn":["0951-7715","1361-6544"]},"doi":"10.1088/1361-6544/aadc12","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1706.07968","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1706.07968"]},"quality_controlled":"1","extern":"1","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"},{"full_name":"Zhang, Ke","last_name":"Zhang","first_name":"Ke"}],"date_created":"2020-09-17T10:42:09Z","date_updated":"2021-01-12T08:19:10Z","volume":31,"year":"2018","publication_status":"published","publisher":"IOP Publishing"},{"publication":"Science Advances","citation":{"ama":"Mas G, Guan J-Y, Crublet E, et al. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 2018;4(9). doi:10.1126/sciadv.aau4196","ista":"Mas G, Guan J-Y, Crublet E, Debled EC, Moriscot C, Gans P, Schoehn G, Macek P, Schanda P, Boisbouvier J. 2018. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 4(9), eaau4196.","ieee":"G. Mas et al., “Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle,” Science Advances, vol. 4, no. 9. American Association for the Advancement of Science, 2018.","apa":"Mas, G., Guan, J.-Y., Crublet, E., Debled, E. C., Moriscot, C., Gans, P., … Boisbouvier, J. (2018). Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aau4196","mla":"Mas, Guillaume, et al. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances, vol. 4, no. 9, eaau4196, American Association for the Advancement of Science, 2018, doi:10.1126/sciadv.aau4196.","short":"G. Mas, J.-Y. Guan, E. Crublet, E.C. Debled, C. Moriscot, P. Gans, G. Schoehn, P. Macek, P. Schanda, J. Boisbouvier, Science Advances 4 (2018).","chicago":"Mas, Guillaume, Jia-Ying Guan, Elodie Crublet, Elisa Colas Debled, Christine Moriscot, Pierre Gans, Guy Schoehn, Pavel Macek, Paul Schanda, and Jerome Boisbouvier. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/sciadv.aau4196."},"article_type":"original","quality_controlled":"1","date_published":"2018-09-19T00:00:00Z","doi":"10.1126/sciadv.aau4196","language":[{"iso":"eng"}],"day":"19","month":"09","publication_identifier":{"issn":["2375-2548"]},"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8437","year":"2018","status":"public","title":"Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle","publication_status":"published","publisher":"American Association for the Advancement of Science","intvolume":" 4","author":[{"full_name":"Mas, Guillaume","last_name":"Mas","first_name":"Guillaume"},{"last_name":"Guan","first_name":"Jia-Ying","full_name":"Guan, Jia-Ying"},{"full_name":"Crublet, Elodie","first_name":"Elodie","last_name":"Crublet"},{"first_name":"Elisa Colas","last_name":"Debled","full_name":"Debled, Elisa Colas"},{"last_name":"Moriscot","first_name":"Christine","full_name":"Moriscot, Christine"},{"last_name":"Gans","first_name":"Pierre","full_name":"Gans, Pierre"},{"full_name":"Schoehn, Guy","last_name":"Schoehn","first_name":"Guy"},{"full_name":"Macek, Pavel","first_name":"Pavel","last_name":"Macek"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Boisbouvier, Jerome","first_name":"Jerome","last_name":"Boisbouvier"}],"date_updated":"2022-08-26T09:11:06Z","date_created":"2020-09-18T10:04:51Z","oa_version":"None","volume":4,"article_number":"eaau4196","type":"journal_article","abstract":[{"lang":"eng","text":"Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action."}],"issue":"9","extern":"1"},{"keyword":["General Biochemistry","Genetics and Molecular Biology"],"month":"11","day":"15","article_processing_charge":"No","publication_identifier":{"issn":["0092-8674"]},"quality_controlled":"1","article_type":"original","page":"1365-1379.e25","publication":"Cell","citation":{"chicago":"Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell. Elsevier, 2018. https://doi.org/10.1016/j.cell.2018.10.039.","short":"K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda, B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen, N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25.","mla":"Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell, vol. 175, no. 5, Elsevier, 2018, p. 1365–1379.e25, doi:10.1016/j.cell.2018.10.039.","apa":"Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., … Schanda, P. (2018). Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. Elsevier. https://doi.org/10.1016/j.cell.2018.10.039","ieee":"K. Weinhäupl et al., “Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space,” Cell, vol. 175, no. 5. Elsevier, p. 1365–1379.e25, 2018.","ista":"Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25.","ama":"Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 2018;175(5):1365-1379.e25. doi:10.1016/j.cell.2018.10.039"},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2018.10.039","date_published":"2018-11-15T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"text":"The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial “transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins in a “nascent chain-like” conformation through a ribosome-free compartment.","lang":"eng"}],"issue":"5","status":"public","publication_status":"published","title":"Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space","publisher":"Elsevier","intvolume":" 175","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8436","year":"2018","date_created":"2020-09-18T10:04:39Z","date_updated":"2021-01-12T08:19:15Z","oa_version":"None","volume":175,"author":[{"full_name":"Weinhäupl, Katharina","first_name":"Katharina","last_name":"Weinhäupl"},{"full_name":"Lindau, Caroline","first_name":"Caroline","last_name":"Lindau"},{"last_name":"Hessel","first_name":"Audrey","full_name":"Hessel, Audrey"},{"full_name":"Wang, Yong","last_name":"Wang","first_name":"Yong"},{"first_name":"Conny","last_name":"Schütze","full_name":"Schütze, Conny"},{"full_name":"Jores, Tobias","first_name":"Tobias","last_name":"Jores"},{"last_name":"Melchionda","first_name":"Laura","full_name":"Melchionda, Laura"},{"full_name":"Schönfisch, Birgit","first_name":"Birgit","last_name":"Schönfisch"},{"first_name":"Hubert","last_name":"Kalbacher","full_name":"Kalbacher, Hubert"},{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"first_name":"Doron","last_name":"Rapaport","full_name":"Rapaport, Doron"},{"last_name":"Brennich","first_name":"Martha","full_name":"Brennich, Martha"},{"full_name":"Lindorff-Larsen, Kresten","first_name":"Kresten","last_name":"Lindorff-Larsen"},{"last_name":"Wiedemann","first_name":"Nils","full_name":"Wiedemann, Nils"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}]},{"oa_version":"Preprint","status":"public","title":"Nonisometric domains with the same Marvizi-Melrose invariants","intvolume":" 23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8426","abstract":[{"text":"For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n.","lang":"eng"}],"type":"journal_article","date_published":"2018-02-05T00:00:00Z","article_type":"original","page":"54-59","publication":"Regular and Chaotic Dynamics","citation":{"short":"L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59.","mla":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics, vol. 23, Springer Nature, 2018, pp. 54–59, doi:10.1134/s1560354718010057.","chicago":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics. Springer Nature, 2018. https://doi.org/10.1134/s1560354718010057.","ama":"Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 2018;23:54-59. doi:10.1134/s1560354718010057","apa":"Buhovsky, L., & Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/s1560354718010057","ieee":"L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” Regular and Chaotic Dynamics, vol. 23. Springer Nature, pp. 54–59, 2018.","ista":"Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59."},"day":"05","article_processing_charge":"No","date_updated":"2021-01-12T08:19:11Z","date_created":"2020-09-17T10:43:21Z","volume":23,"author":[{"full_name":"Buhovsky, Lev","first_name":"Lev","last_name":"Buhovsky"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"}],"publication_status":"published","publisher":"Springer Nature","year":"2018","extern":"1","language":[{"iso":"eng"}],"doi":"10.1134/s1560354718010057","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1801.00952"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.00952"}],"month":"02","publication_identifier":{"issn":["1560-3547","1468-4845"]}},{"type":"journal_article","issue":"9","extern":"1","_id":"8438","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","status":"public","title":"Dynamics and interactions of AAC3 in DPC are not functionally relevant","publication_status":"published","publisher":"Springer Nature","intvolume":" 25","author":[{"last_name":"Kurauskas","first_name":"Vilius","full_name":"Kurauskas, Vilius"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"date_updated":"2021-01-12T08:19:16Z","date_created":"2020-09-18T10:04:59Z","volume":25,"oa_version":"None","keyword":["Molecular Biology","Structural Biology"],"day":"03","month":"09","publication_identifier":{"issn":["1545-9993","1545-9985"]},"article_processing_charge":"No","publication":"Nature Structural & Molecular Biology","citation":{"chicago":"Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology. Springer Nature, 2018. https://doi.org/10.1038/s41594-018-0127-4.","mla":"Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology, vol. 25, no. 9, Springer Nature, 2018, pp. 745–47, doi:10.1038/s41594-018-0127-4.","short":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature Structural & Molecular Biology 25 (2018) 745–747.","ista":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 25(9), 745–747.","ieee":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics and interactions of AAC3 in DPC are not functionally relevant,” Nature Structural & Molecular Biology, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018.","apa":"Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., & Schanda, P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-018-0127-4","ama":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 2018;25(9):745-747. doi:10.1038/s41594-018-0127-4"},"article_type":"letter_note","quality_controlled":"1","page":"745-747","doi":"10.1038/s41594-018-0127-4","date_published":"2018-09-03T00:00:00Z","language":[{"iso":"eng"}]},{"month":"12","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"doi":"10.1039/c8sm01760c","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1909.11121","open_access":"1"}],"external_id":{"arxiv":["1909.11121"],"pmid":["30456407"]},"oa":1,"quality_controlled":"1","extern":"1","author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci"}],"date_updated":"2023-02-23T13:47:43Z","date_created":"2021-02-01T13:44:41Z","volume":14,"year":"2018","pmid":1,"publication_status":"published","publisher":"Royal Society of Chemistry ","day":"21","article_processing_charge":"No","scopus_import":"1","keyword":["General Chemistry","Condensed Matter Physics"],"date_published":"2018-12-21T00:00:00Z","publication":"Soft Matter","citation":{"apa":"Aubret, A., & Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c8sm01760c","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” Soft Matter, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018.","ista":"Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588.","ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 2018;14(47):9577-9588. doi:10.1039/c8sm01760c","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter. Royal Society of Chemistry , 2018. https://doi.org/10.1039/c8sm01760c.","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588.","mla":"Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:10.1039/c8sm01760c."},"article_type":"original","page":"9577-9588","abstract":[{"lang":"eng","text":"The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena."}],"issue":"47","type":"journal_article","oa_version":"Preprint","_id":"9053","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","status":"public","intvolume":" 14"},{"publication_identifier":{"issn":["0935-9648","1521-4095"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1002/adma.201805564","quality_controlled":"1","external_id":{"arxiv":["1811.04562"]},"extern":"1","article_number":"1805564","volume":30,"date_updated":"2021-02-03T13:58:39Z","date_created":"2021-02-02T15:50:58Z","author":[{"full_name":"Lee, Nara","last_name":"Lee","first_name":"Nara"},{"first_name":"Eunjung","last_name":"Ko","full_name":"Ko, Eunjung"},{"full_name":"Choi, Hwan Young","last_name":"Choi","first_name":"Hwan Young"},{"last_name":"Hong","first_name":"Yun Jeong","full_name":"Hong, Yun Jeong"},{"full_name":"Nauman, Muhammad","last_name":"Nauman","first_name":"Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"},{"full_name":"Kang, Woun","last_name":"Kang","first_name":"Woun"},{"full_name":"Choi, Hyoung Joon","last_name":"Choi","first_name":"Hyoung Joon"},{"last_name":"Choi","first_name":"Young Jai","full_name":"Choi, Young Jai"},{"last_name":"Jo","first_name":"Younjung","full_name":"Jo, Younjung"}],"publisher":"Wiley","publication_status":"published","year":"2018","article_processing_charge":"No","day":"29","keyword":["Mechanical Engineering","General Materials Science","Mechanics of Materials"],"date_published":"2018-10-29T00:00:00Z","article_type":"original","citation":{"ama":"Lee N, Ko E, Choi HY, et al. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 2018;30(52). doi:10.1002/adma.201805564","ista":"Lee N, Ko E, Choi HY, Hong YJ, Nauman M, Kang W, Choi HJ, Choi YJ, Jo Y. 2018. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 30(52), 1805564.","ieee":"N. Lee et al., “Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate,” Advanced Materials, vol. 30, no. 52. Wiley, 2018.","apa":"Lee, N., Ko, E., Choi, H. Y., Hong, Y. J., Nauman, M., Kang, W., … Jo, Y. (2018). Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201805564","mla":"Lee, Nara, et al. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” Advanced Materials, vol. 30, no. 52, 1805564, Wiley, 2018, doi:10.1002/adma.201805564.","short":"N. Lee, E. Ko, H.Y. Choi, Y.J. Hong, M. Nauman, W. Kang, H.J. Choi, Y.J. Choi, Y. Jo, Advanced Materials 30 (2018).","chicago":"Lee, Nara, Eunjung Ko, Hwan Young Choi, Yun Jeong Hong, Muhammad Nauman, Woun Kang, Hyoung Joon Choi, Young Jai Choi, and Younjung Jo. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201805564."},"publication":"Advanced Materials","issue":"52","abstract":[{"lang":"eng","text":"The novel electronic state of the canted antiferromagnetic (AFM) insulator, strontium iridate (Sr2IrO4) has been well described by the spin-orbit-entangled isospin Jeff = 1/2, but the role of isospin in transport phenomena remains poorly understood. In this study, antiferromagnet-based spintronic functionality is demonstrated by combining unique characteristics of the isospin state in Sr2IrO4. Based on magnetic and transport measurements, large and highly anisotropic magnetoresistance (AMR) is obtained by manipulating the antiferromagnetic isospin domains. First-principles calculations suggest that electrons whose isospin directions are strongly coupled to in-plane net magnetic moment encounter the isospin mismatch when moving across antiferromagnetic domain boundaries, which generates a high resistance state. By rotating a magnetic field that aligns in-plane net moments and removes domain boundaries, the macroscopically-ordered isospins govern dynamic transport through the system, which leads to the extremely angle-sensitive AMR. As with this work that establishes a link between isospins and magnetotransport in strongly spin-orbit-coupled AFM Sr2IrO4, the peculiar AMR effect provides a beneficial foundation for fundamental and applied research on AFM spintronics."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 30","status":"public","title":"Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9066"},{"_id":"9068","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se","publication_status":"published","publisher":"Elsevier","intvolume":" 536","author":[{"full_name":"Hussain, Tayyaba","last_name":"Hussain","first_name":"Tayyaba"},{"last_name":"Oh","first_name":"Myeong-jun","full_name":"Oh, Myeong-jun"},{"full_name":"Nauman, Muhammad","last_name":"Nauman","first_name":"Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"},{"full_name":"Jo, Younjung","last_name":"Jo","first_name":"Younjung"},{"first_name":"Garam","last_name":"Han","full_name":"Han, Garam"},{"full_name":"Kim, Changyoung","last_name":"Kim","first_name":"Changyoung"},{"last_name":"Kang","first_name":"Woun","full_name":"Kang, Woun"}],"date_updated":"2021-02-04T07:18:57Z","date_created":"2021-02-02T15:52:43Z","volume":536,"oa_version":"None","type":"journal_article","abstract":[{"text":"We report the temperature-dependent resistivity ρ(T) of chalcogenide NiS2-xSex (x = 0.1) using hydrostatic pressure as a control parameter in the temperature range of 4–300 K. The insulating behavior of ρ(T) survives at low temperatures in the pressure regime below 7.5 kbar, whereas a clear insulator-to-metallic transition is observed above 7.5 kbar. Two types of magnetic transitions, from the paramagnetic (PM) to the antiferromagnetic (AFM) state and from the AFM state to the weak ferromagnetic (WF) state, were evaluated and confirmed by magnetization measurement. According to the temperature–pressure phase diagram, the WF phase survives up to 7.5 kbar, and the transition temperature of the WF transition decreases as the pressure increases, whereas the metal–insulator transition temperature increases up to 9.4 kbar. We analyzed the metallic behavior and proposed Fermi-liquid behavior of NiS1.9Se0.1.","lang":"eng"}],"extern":"1","publication":"Physica B: Condensed Matter","citation":{"ieee":"T. Hussain et al., “Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se,” Physica B: Condensed Matter, vol. 536. Elsevier, pp. 235–238, 2018.","apa":"Hussain, T., Oh, M., Nauman, M., Jo, Y., Han, G., Kim, C., & Kang, W. (2018). Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2017.11.032","ista":"Hussain T, Oh M, Nauman M, Jo Y, Han G, Kim C, Kang W. 2018. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 536, 235–238.","ama":"Hussain T, Oh M, Nauman M, et al. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 2018;536:235-238. doi:10.1016/j.physb.2017.11.032","chicago":"Hussain, Tayyaba, Myeong-jun Oh, Muhammad Nauman, Younjung Jo, Garam Han, Changyoung Kim, and Woun Kang. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” Physica B: Condensed Matter. Elsevier, 2018. https://doi.org/10.1016/j.physb.2017.11.032.","short":"T. Hussain, M. Oh, M. Nauman, Y. Jo, G. Han, C. Kim, W. Kang, Physica B: Condensed Matter 536 (2018) 235–238.","mla":"Hussain, Tayyaba, et al. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” Physica B: Condensed Matter, vol. 536, Elsevier, 2018, pp. 235–38, doi:10.1016/j.physb.2017.11.032."},"article_type":"original","quality_controlled":"1","page":"235-238","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.physb.2017.11.032","language":[{"iso":"eng"}],"month":"05","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0921-4526"]}}]