[{"publication":"Heredity","doi":"10.1038/hdy.2016.25","page":"51-61","oa_version":"None","_id":"7736","publisher":"Springer Nature","date_created":"2020-04-30T10:50:03Z","day":"04","title":"EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations","date_updated":"2021-01-12T08:15:11Z","publication_identifier":{"issn":["0018-067X","1365-2540"]},"month":"05","author":[{"first_name":"G-B","last_name":"Chen","full_name":"Chen, G-B"},{"first_name":"S H","full_name":"Lee, S H","last_name":"Lee"},{"full_name":"Zhu, Z-X","last_name":"Zhu","first_name":"Z-X"},{"full_name":"Benyamin, B","last_name":"Benyamin","first_name":"B"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}],"date_published":"2016-05-04T00:00:00Z","year":"2016","article_processing_charge":"No","type":"journal_article","citation":{"ieee":"G.-B. Chen, S. H. Lee, Z.-X. Zhu, B. Benyamin, and M. R. Robinson, “EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations,” <i>Heredity</i>, vol. 117. Springer Nature, pp. 51–61, 2016.","short":"G.-B. Chen, S.H. Lee, Z.-X. Zhu, B. Benyamin, M.R. Robinson, Heredity 117 (2016) 51–61.","apa":"Chen, G.-B., Lee, S. H., Zhu, Z.-X., Benyamin, B., &#38; Robinson, M. R. (2016). EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. <i>Heredity</i>. Springer Nature. <a href=\"https://doi.org/10.1038/hdy.2016.25\">https://doi.org/10.1038/hdy.2016.25</a>","mla":"Chen, G. B., et al. “EigenGWAS: Finding Loci under Selection through Genome-Wide Association Studies of Eigenvectors in Structured Populations.” <i>Heredity</i>, vol. 117, Springer Nature, 2016, pp. 51–61, doi:<a href=\"https://doi.org/10.1038/hdy.2016.25\">10.1038/hdy.2016.25</a>.","ista":"Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. 2016. EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. Heredity. 117, 51–61.","chicago":"Chen, G-B, S H Lee, Z-X Zhu, B Benyamin, and Matthew Richard Robinson. “EigenGWAS: Finding Loci under Selection through Genome-Wide Association Studies of Eigenvectors in Structured Populations.” <i>Heredity</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/hdy.2016.25\">https://doi.org/10.1038/hdy.2016.25</a>.","ama":"Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. <i>Heredity</i>. 2016;117:51-61. doi:<a href=\"https://doi.org/10.1038/hdy.2016.25\">10.1038/hdy.2016.25</a>"},"extern":"1","article_type":"original","publication_status":"published","volume":117,"abstract":[{"text":"We develop a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient. By combining the statistical framework for genome-wide association studies (GWASs) with eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterize the structure of genetic data, loci under selection can be identified without a requirement for discrete populations. We show through theory and simulation that our approach can identify regions under selection along gradients of ancestry, and in real data we confirm this by demonstrating LCT to be under selection between HapMap CEU–TSI cohorts, and we then validate this selection signal across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU–TSI cohort and within the POPRES sample, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. Controlling for population stratification is of great importance in any quantitative genetic study and our approach also provides a simple, fast and accurate way of predicting principal components in independent samples. With ever increasing sample sizes across many fields, this approach is likely to be greatly utilized to gain individual-level eigenvectors avoiding the computational challenges associated with conducting singular value decomposition in large data sets. We have developed freely available software, Genetic Analysis Repository (GEAR), to facilitate the application of the methods.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       117"},{"extern":"1","oa":1,"intvolume":"        48","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"5","main_file_link":[{"url":"https://doi.org/10.1038/ng.3538","open_access":"1"}],"volume":48,"_id":"7737","date_created":"2020-04-30T10:50:26Z","publication":"Nature Genetics","page":"481-487","article_processing_charge":"No","date_published":"2016-03-28T00:00:00Z","date_updated":"2021-01-12T08:15:11Z","title":"Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets","month":"03","article_type":"original","citation":{"ieee":"Z. Zhu <i>et al.</i>, “Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets,” <i>Nature Genetics</i>, vol. 48, no. 5. Springer Nature, pp. 481–487, 2016.","apa":"Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., … Yang, J. (2016). Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>","short":"Z. Zhu, F. Zhang, H. Hu, A. Bakshi, M.R. Robinson, J.E. Powell, G.W. Montgomery, M.E. Goddard, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 48 (2016) 481–487.","ista":"Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard ME, Wray NR, Visscher PM, Yang J. 2016. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics. 48(5), 481–487.","mla":"Zhu, Zhihong, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>, vol. 48, no. 5, Springer Nature, 2016, pp. 481–87, doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>.","ama":"Zhu Z, Zhang F, Hu H, et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. 2016;48(5):481-487. doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>","chicago":"Zhu, Zhihong, Futao Zhang, Han Hu, Andrew Bakshi, Matthew Richard Robinson, Joseph E Powell, Grant W Montgomery, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>."},"type":"journal_article","quality_controlled":"1","abstract":[{"text":"Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"publisher":"Springer Nature","day":"28","doi":"10.1038/ng.3538","oa_version":"Published Version","year":"2016","author":[{"full_name":"Zhu, Zhihong","last_name":"Zhu","first_name":"Zhihong"},{"last_name":"Zhang","full_name":"Zhang, Futao","first_name":"Futao"},{"first_name":"Han","last_name":"Hu","full_name":"Hu, Han"},{"full_name":"Bakshi, Andrew","last_name":"Bakshi","first_name":"Andrew"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Joseph E","full_name":"Powell, Joseph E","last_name":"Powell"},{"first_name":"Grant W","full_name":"Montgomery, Grant W","last_name":"Montgomery"},{"last_name":"Goddard","full_name":"Goddard, Michael E","first_name":"Michael E"},{"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","full_name":"Yang, Jian","first_name":"Jian"}],"publication_identifier":{"issn":["1061-4036","1546-1718"]}},{"article_processing_charge":"No","year":"2016","author":[{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Andrea J.","full_name":"Liu, Andrea J.","last_name":"Liu"},{"last_name":"Sethna","full_name":"Sethna, James P.","first_name":"James P."}],"date_published":"2016-08-30T00:00:00Z","month":"08","publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_updated":"2021-01-12T08:15:21Z","title":"Scaling ansatz for the jamming transition","day":"30","date_created":"2020-04-30T11:39:53Z","_id":"7760","publisher":"Proceedings of the National Academy of Sciences","page":"9745-9750","oa_version":"None","doi":"10.1073/pnas.1601858113","publication":"Proceedings of the National Academy of Sciences","intvolume":"       113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"35","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"volume":113,"abstract":[{"lang":"eng","text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming."}],"publication_status":"published","article_type":"original","extern":"1","type":"journal_article","citation":{"ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(35):9745-9750. doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>.","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750.","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750.","apa":"Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016."}},{"title":"Pinning susceptibility: The effect of dilute, quenched disorder on jamming","date_updated":"2021-01-12T08:15:21Z","publication_identifier":{"issn":["0031-9007","1079-7114"]},"month":"06","author":[{"first_name":"Amy L.","last_name":"Graves","full_name":"Graves, Amy L."},{"last_name":"Nashed","full_name":"Nashed, Samer","first_name":"Samer"},{"last_name":"Padgett","full_name":"Padgett, Elliot","first_name":"Elliot"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"first_name":"James P.","full_name":"Sethna, James P.","last_name":"Sethna"}],"date_published":"2016-06-10T00:00:00Z","year":"2016","article_processing_charge":"No","publication":"Physical Review Letters","doi":"10.1103/physrevlett.116.235501","oa_version":"None","publisher":"American Physical Society","_id":"7761","date_created":"2020-04-30T11:40:10Z","day":"10","publication_status":"published","abstract":[{"text":"We study the effect of dilute pinning on the jamming transition. Pinning reduces the average contact number needed to jam unpinned particles and shifts the jamming threshold to lower densities, leading to a pinning susceptibility, χp. Our main results are that this susceptibility obeys scaling form and diverges in the thermodynamic limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins. Finite-size scaling arguments yield these values with associated statistical (systematic) errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic corrections raise the exponent in d=2 to close to the d=3 value, although the systematic errors are very large.","lang":"eng"}],"volume":116,"language":[{"iso":"eng"}],"status":"public","article_number":"235501","quality_controlled":"1","issue":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       116","type":"journal_article","citation":{"short":"A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna, Physical Review Letters 116 (2016).","apa":"Graves, A. L., Nashed, S., Padgett, E., Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>","ieee":"A. L. Graves, S. Nashed, E. Padgett, C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Pinning susceptibility: The effect of dilute, quenched disorder on jamming,” <i>Physical Review Letters</i>, vol. 116, no. 23. American Physical Society, 2016.","ama":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. 2016;116(23). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>","chicago":"Graves, Amy L., Samer Nashed, Elliot Padgett, Carl Peter Goodrich, Andrea J. Liu, and James P. Sethna. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>.","mla":"Graves, Amy L., et al. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>, vol. 116, no. 23, 235501, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>.","ista":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. 2016. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. 116(23), 235501."},"extern":"1","article_type":"original"},{"article_processing_charge":"No","year":"2016","author":[{"full_name":"Rieser, Jennifer M.","last_name":"Rieser","first_name":"Jennifer M."},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"first_name":"Douglas J.","last_name":"Durian","full_name":"Durian, Douglas J."}],"date_published":"2016-02-23T00:00:00Z","publication_identifier":{"issn":["0031-9007","1079-7114"]},"title":"Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials","date_updated":"2021-01-12T08:15:22Z","month":"02","publisher":"American Physical Society","_id":"7762","day":"23","date_created":"2020-04-30T11:40:25Z","publication":"Physical Review Letters","doi":"10.1103/physrevlett.116.088001","oa_version":"None","quality_controlled":"1","article_number":"088001 ","intvolume":"       116","issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition.","lang":"eng"}],"publication_status":"published","volume":116,"status":"public","language":[{"iso":"eng"}],"article_type":"original","extern":"1","citation":{"short":"J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters 116 (2016).","apa":"Rieser, J. M., Goodrich, C. P., Liu, A. J., &#38; Durian, D. J. (2016). Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>","ieee":"J. M. Rieser, C. P. Goodrich, A. J. Liu, and D. J. Durian, “Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials,” <i>Physical Review Letters</i>, vol. 116, no. 8. American Physical Society, 2016.","chicago":"Rieser, Jennifer M., Carl Peter Goodrich, Andrea J. Liu, and Douglas J. Durian. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>.","ama":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. 2016;116(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>","ista":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. 2016. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. 116(8), 088001.","mla":"Rieser, Jennifer M., et al. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>, vol. 116, no. 8, 088001, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>."},"type":"journal_article"},{"publisher":"Elsevier","_id":"7763","day":"15","date_created":"2020-04-30T11:40:41Z","doi":"10.1016/j.jcp.2015.10.035","publication":"Journal of Computational Physics","oa_version":"None","page":"244-262","year":"2016","article_processing_charge":"No","author":[{"first_name":"Richard","full_name":"Lombardini, Richard","last_name":"Lombardini"},{"first_name":"Ramiro","full_name":"Acevedo, Ramiro","last_name":"Acevedo"},{"first_name":"Alexander","full_name":"Kuczala, Alexander","last_name":"Kuczala"},{"last_name":"Keys","full_name":"Keys, Kerry P.","first_name":"Kerry P."},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"first_name":"Bruce R.","last_name":"Johnson","full_name":"Johnson, Bruce R."}],"date_published":"2016-01-15T00:00:00Z","publication_identifier":{"issn":["0021-9991"]},"date_updated":"2021-01-12T08:15:22Z","title":"Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena","month":"01","article_type":"original","extern":"1","citation":{"chicago":"Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys, Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>.","ama":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. 2016;305:244-262. doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>","mla":"Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>, vol. 305, Elsevier, 2016, pp. 244–62, doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>.","ista":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. 305, 244–262.","short":"R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson, Journal of Computational Physics 305 (2016) 244–262.","apa":"Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., &#38; Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>","ieee":"R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B. R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena,” <i>Journal of Computational Physics</i>, vol. 305. Elsevier, pp. 244–262, 2016."},"type":"journal_article","quality_controlled":"1","intvolume":"       305","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"An orthogonal wavelet basis is characterized by its approximation order, which relates to the ability of the basis to represent general smooth functions on a given scale. It is known, though perhaps not widely known, that there are ways of exceeding the approximation order, i.e., achieving higher-order error in the discretized wavelet transform and its inverse. The focus here is on the development of a practical formulation to accomplish this first for 1D smooth functions, then for 1D functions with discontinuities and then for multidimensional (here 2D) functions with discontinuities. It is shown how to transcend both the wavelet approximation order and the 2D Gibbs phenomenon in representing electromagnetic fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis grid.","lang":"eng"}],"publication_status":"published","volume":305,"status":"public","language":[{"iso":"eng"}]},{"related_material":{"link":[{"relation":"other","url":"https://doi.org/10.1039/c6sm02496c"}]},"volume":12,"publication_status":"published","abstract":[{"text":"States of self stress, organizations of internal forces in many-body systems that are in equilibrium with an absence of external forces, can be thought of as the constitutive building blocks of the elastic response of a material. In overconstrained disordered packings they have a natural mathematical correspondence with the zero-energy vibrational modes in underconstrained systems. While substantial attention in the literature has been paid to diverging length scales associated with zero- and finite-energy vibrational modes in jammed systems, less is known about the spatial structure of the states of self stress. In this work we define a natural way in which a unique state of self stress can be associated with each bond in a disordered spring network derived from a jammed packing, and then investigate the spatial structure of these bond-localized states of self stress. This allows for an understanding of how the elastic properties of a system would change upon changing the strength or even existence of any bond in the system.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        12","issue":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","citation":{"ama":"Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. 2016;12(17):3982-3990. doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>","chicago":"Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>.","mla":"Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>, vol. 12, no. 17, Royal Society of Chemistry, 2016, pp. 3982–90, doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>.","ista":"Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self stress in jammed systems. Soft Matter. 12(17), 3982–3990.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990.","apa":"Sussman, D. M., Goodrich, C. P., &#38; Liu, A. J. (2016). Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>","ieee":"D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states of self stress in jammed systems,” <i>Soft Matter</i>, vol. 12, no. 17. Royal Society of Chemistry, pp. 3982–3990, 2016."},"article_type":"original","publication_identifier":{"issn":["1744-683X","1744-6848"]},"date_updated":"2021-01-12T08:15:22Z","title":"Spatial structure of states of self stress in jammed systems","month":"03","year":"2016","article_processing_charge":"No","author":[{"first_name":"Daniel M.","full_name":"Sussman, Daniel M.","last_name":"Sussman"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."}],"date_published":"2016-03-14T00:00:00Z","doi":"10.1039/c6sm00094k","publication":"Soft Matter","oa_version":"None","page":"3982-3990","publisher":"Royal Society of Chemistry","_id":"7764","day":"14","date_created":"2020-04-30T11:40:56Z"},{"extern":"1","type":"conference","scopus_import":"1","citation":{"ieee":"S. Haider, W. Hasenplaugh, and D.-A. Alistarh, “Lease/Release: Architectural support for scaling contended data structures,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2016, vol. 12-16-March-2016.","short":"S. Haider, W. Hasenplaugh, D.-A. Alistarh, in:, ACM, 2016.","apa":"Haider, S., Hasenplaugh, W., &#38; Alistarh, D.-A. (2016). Lease/Release: Architectural support for scaling contended data structures (Vol. 12-16-March-2016). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. <a href=\"https://doi.org/10.1145/2851141.2851155\">https://doi.org/10.1145/2851141.2851155</a>","mla":"Haider, Syed, et al. <i>Lease/Release: Architectural Support for Scaling Contended Data Structures</i>. Vol. 12-16-March-2016, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2851141.2851155\">10.1145/2851141.2851155</a>.","ista":"Haider S, Hasenplaugh W, Alistarh D-A. 2016. Lease/Release: Architectural support for scaling contended data structures. PPoPP: Principles and Practice of Parallel Pogramming vol. 12-16-March-2016.","chicago":"Haider, Syed, William Hasenplaugh, and Dan-Adrian Alistarh. “Lease/Release: Architectural Support for Scaling Contended Data Structures,” Vol. 12-16-March-2016. ACM, 2016. <a href=\"https://doi.org/10.1145/2851141.2851155\">https://doi.org/10.1145/2851141.2851155</a>.","ama":"Haider S, Hasenplaugh W, Alistarh D-A. Lease/Release: Architectural support for scaling contended data structures. In: Vol 12-16-March-2016. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2851141.2851155\">10.1145/2851141.2851155</a>"},"status":"public","language":[{"iso":"eng"}],"publist_id":"6871","volume":"12-16-March-2016","publication_status":"published","abstract":[{"lang":"eng","text":"High memory contention is generally agreed to be a worst-case scenario for concurrent data structures. There has been a significant amount of research effort spent investigating designs which minimize contention, and several programming techniques have been proposed to mitigate its effects. However, there are currently few architectural mechanisms to allow scaling contended data structures at high thread counts. In this paper, we investigate hardware support for scalable contended data structures. We propose Lease/Release, a simple addition to standard directory-based MSI cache coherence protocols, allowing participants to lease memory, at the granularity of cache lines, by delaying coherence messages for a short, bounded period of time. Our analysis shows that Lease/Release can significantly reduce the overheads of contention for both non-blocking (lock-free) and lock-based data structure implementations, while ensuring that no deadlocks are introduced. We validate Lease/Release empirically on the Graphite multiprocessor simulator, on a range of data structures, including queue, stack, and priority queue implementations, as well as on transactional applications. Results show that Lease/Release consistently improves both throughput and energy usage, by up to 5x, both for lock-free and lock-based data structure designs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank Richard Black, Miguel Castro, Dave Dice, Aleksandar Dragojevic, Maurice Herlihy, Ant Rowstron, Nir Shavit, and Vasileios Trigonakis, as well as the anonymous reviewers, for helpful suggestions during the development of this paper.","quality_controlled":"1","oa_version":"None","doi":"10.1145/2851141.2851155","day":"27","date_created":"2018-12-11T11:48:29Z","publisher":"ACM","_id":"785","month":"02","date_updated":"2022-03-18T12:56:29Z","title":"Lease/Release: Architectural support for scaling contended data structures","year":"2016","conference":{"name":"PPoPP: Principles and Practice of Parallel Pogramming"},"article_processing_charge":"No","author":[{"first_name":"Syed","full_name":"Haider, Syed","last_name":"Haider"},{"full_name":"Hasenplaugh, William","last_name":"Hasenplaugh","first_name":"William"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"date_published":"2016-02-27T00:00:00Z"},{"volume":63,"main_file_link":[{"url":"https://arxiv.org/abs/1311.3200","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Part of this work was performed while the first author was a postdoctoral associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations. The second author was supported in part by ISF grant 1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926, IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923, and by equipment grants from Intel Corporation.","issue":"4","intvolume":"        63","oa":1,"extern":"1","month":"09","date_updated":"2023-02-23T13:19:04Z","title":"Are lock free concurrent algorithms practically wait free ","date_published":"2016-09-01T00:00:00Z","article_processing_charge":"No","publication":"Journal of the ACM","date_created":"2018-12-11T11:48:29Z","external_id":{"arxiv":["1311.3200"]},"_id":"786","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. Although obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most nonblocking commercial code is only lock-free. This article suggests a simple solution to this problem.We show that for a large class of lock-free algorithms, under scheduling conditions that approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can continue to design simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes to the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1 but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst-case adversary, in a stochastic model capturing their expected asymptotic behavior."}],"publication_status":"published","publist_id":"6870","quality_controlled":"1","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically Wait Free .” <i>Journal of the ACM</i>, vol. 63, no. 4, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2903136\">10.1145/2903136</a>.","ista":"Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms practically wait free . Journal of the ACM. 63(4).","chicago":"Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free Concurrent Algorithms Practically Wait Free .” <i>Journal of the ACM</i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2903136\">https://doi.org/10.1145/2903136</a>.","ama":"Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms practically wait free . <i>Journal of the ACM</i>. 2016;63(4). doi:<a href=\"https://doi.org/10.1145/2903136\">10.1145/2903136</a>","ieee":"D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent algorithms practically wait free ,” <i>Journal of the ACM</i>, vol. 63, no. 4. ACM, 2016.","short":"D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016).","apa":"Alistarh, D.-A., Censor Hillel, K., &#38; Shavit, N. (2016). Are lock free concurrent algorithms practically wait free . <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2903136\">https://doi.org/10.1145/2903136</a>"},"type":"journal_article","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Censor Hillel","full_name":"Censor Hillel, Keren","first_name":"Keren"},{"last_name":"Shavit","full_name":"Shavit, Nir","first_name":"Nir"}],"year":"2016","arxiv":1,"oa_version":"Preprint","doi":"10.1145/2903136","day":"01","publisher":"ACM"},{"intvolume":"        90","oa":1,"issue":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","volume":90,"extern":"1","article_processing_charge":"No","date_published":"2016-04-06T00:00:00Z","date_updated":"2021-01-12T08:16:34Z","title":"Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories","month":"04","_id":"8020","external_id":{"pmid":["26996082"]},"date_created":"2020-06-25T13:05:33Z","publication":"Neuron","file_date_updated":"2020-07-14T12:48:08Z","page":"191-203","quality_controlled":"1","publication_status":"published","abstract":[{"text":"Balance of cortical excitation and inhibition (EI) is thought to be disrupted in several neuropsychiatric conditions, yet it is not clear how it is maintained in the healthy human brain. When EI balance is disturbed during learning and memory in animal models, it can be restabilized via formation of inhibitory replicas of newly formed excitatory connections. Here we assess evidence for such selective inhibitory rebalancing in humans. Using fMRI repetition suppression we measure newly formed cortical associations in the human brain. We show that expression of these associations reduces over time despite persistence in behavior, consistent with inhibitory rebalancing. To test this, we modulated excitation/inhibition balance with transcranial direct current stimulation (tDCS). Using ultra-high-field (7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations to be re-expressed. This suggests that in humans associative memories are stored in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory connections are unmasked.","lang":"eng"}],"status":"public","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["570"],"article_type":"original","file":[{"date_created":"2020-07-09T09:57:04Z","creator":"cziletti","file_id":"8104","access_level":"open_access","file_name":"2016_Neuron_Barron.pdf","date_updated":"2020-07-14T12:48:08Z","content_type":"application/pdf","file_size":5334136,"checksum":"9ce7a1c64986dce0435c070285a7ef9b","relation":"main_file"}],"type":"journal_article","citation":{"chicago":"Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” <i>Neuron</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">https://doi.org/10.1016/j.neuron.2016.02.031</a>.","ama":"Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. <i>Neuron</i>. 2016;90(1):191-203. doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">10.1016/j.neuron.2016.02.031</a>","mla":"Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” <i>Neuron</i>, vol. 90, no. 1, Elsevier, 2016, pp. 191–203, doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">10.1016/j.neuron.2016.02.031</a>.","ista":"Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. Neuron. 90(1), 191–203.","apa":"Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare, S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">https://doi.org/10.1016/j.neuron.2016.02.031</a>","short":"H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.","ieee":"H. C. Barron <i>et al.</i>, “Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories,” <i>Neuron</i>, vol. 90, no. 1. Elsevier, pp. 191–203, 2016."},"year":"2016","author":[{"first_name":"H.C.","last_name":"Barron","full_name":"Barron, H.C."},{"last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"},{"full_name":"Emir, U.E.","last_name":"Emir","first_name":"U.E."},{"full_name":"Makin, T.R.","last_name":"Makin","first_name":"T.R."},{"full_name":"O’Shea, J.","last_name":"O’Shea","first_name":"J."},{"last_name":"Clare","full_name":"Clare, S.","first_name":"S."},{"last_name":"Jbabdi","full_name":"Jbabdi, S.","first_name":"S."},{"first_name":"R.J.","last_name":"Dolan","full_name":"Dolan, R.J."},{"last_name":"Behrens","full_name":"Behrens, T.E.J.","first_name":"T.E.J."}],"publication_identifier":{"issn":["0896-6273"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","day":"06","doi":"10.1016/j.neuron.2016.02.031","oa_version":"Published Version"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_identifier":{"isbn":["9780262339360"]},"year":"2016","conference":{"end_date":"2016-07-08","location":"Cancun, Mexico","start_date":"2016-07-04","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems"},"author":[{"full_name":"Martius, Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"full_name":"Hostettler, Rafael","last_name":"Hostettler","first_name":"Rafael"},{"first_name":"Alois","full_name":"Knoll, Alois","last_name":"Knoll"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}],"oa_version":"Published Version","doi":"10.7551/978-0-262-33936-0-ch029","day":"01","publisher":"MIT Press","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"quality_controlled":"1","citation":{"chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>Proceedings of the Artificial Life Conference 2016</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>Proceedings of the Artificial Life Conference 2016</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>Proceedings of the Artificial Life Conference 2016</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>Proceedings of the Artificial Life Conference 2016</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>Proceedings of the Artificial Life Conference 2016</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143."},"type":"conference","file":[{"checksum":"cff63e7a4b8ac466ba51a9c84153a940","relation":"main_file","date_updated":"2020-07-14T12:48:09Z","content_type":"application/pdf","file_size":678670,"file_name":"2016_ProcALIFE_Martius.pdf","access_level":"open_access","file_id":"8096","date_created":"2020-07-06T12:59:09Z","creator":"cziletti"}],"ddc":["610"],"month":"09","date_updated":"2021-01-12T08:16:53Z","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","ec_funded":1,"article_processing_charge":"No","date_published":"2016-09-01T00:00:00Z","page":"142-143","publication":"Proceedings of the Artificial Life Conference 2016","file_date_updated":"2020-07-14T12:48:09Z","date_created":"2020-07-05T22:00:47Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"_id":"8094","volume":28,"intvolume":"        28","oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","scopus_import":1},{"year":"2016","article_processing_charge":"No","author":[{"first_name":"Claudia","full_name":"Clopath, Claudia","last_name":"Clopath"},{"last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Froemke","full_name":"Froemke, Robert C.","first_name":"Robert C."},{"last_name":"Sprekeler","full_name":"Sprekeler, Henning","first_name":"Henning"}],"date_published":"2016-07-29T00:00:00Z","title":"Receptive field formation by interacting excitatory and inhibitory synaptic plasticity","date_updated":"2021-01-12T08:17:02Z","month":"07","publisher":"Cold Spring Harbor Laboratory","_id":"8128","day":"29","date_created":"2020-07-16T12:26:55Z","publication":"bioRxiv","page":"43","oa_version":"Preprint","oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","main_file_link":[{"url":"https://doi.org/10.1101/066589 ","open_access":"1"}],"abstract":[{"lang":"eng","text":"The stimulus selectivity of synaptic currents in cortical neurons often shows a co-tuning of excitation and inhibition, but the mechanisms that underlie the emergence and plasticity of this co-tuning are not fully understood. Using a computational model, we show that an interaction of excitatory and inhibitory synaptic plasticity reproduces both the developmental and – when combined with a disinhibitory gate – the adult plasticity of excitatory and inhibitory receptive fields in auditory cortex. The co-tuning arises from inhibitory plasticity that balances excitation and inhibition, while excitatory stimulus selectivity can result from two different mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus selectivity at the cost of a broader inhibitory receptive field. Alternatively, input asymmetries can be amplified by synaptic competition. The latter leaves any receptive field plasticity transient, a prediction we verify in recordings in auditory cortex."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"extern":"1","citation":{"ieee":"C. Clopath, T. P. Vogels, R. C. Froemke, and H. Sprekeler, “Receptive field formation by interacting excitatory and inhibitory synaptic plasticity,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2016.","short":"C. Clopath, T.P. Vogels, R.C. Froemke, H. Sprekeler, BioRxiv (2016).","apa":"Clopath, C., Vogels, T. P., Froemke, R. C., &#38; Sprekeler, H. (2016). Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. 2016. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. bioRxiv, .","mla":"Clopath, Claudia, et al. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2016.","ama":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. 2016.","chicago":"Clopath, Claudia, Tim P Vogels, Robert C. Froemke, and Henning Sprekeler. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2016."},"type":"preprint"},{"publisher":"ASM","_id":"813","day":"01","date_created":"2018-12-11T11:48:38Z","doi":"10.1128/JVI.03197-15","publication":"Journal of Virology","page":"4593 - 4603","year":"2016","date_published":"2016-05-01T00:00:00Z","author":[{"full_name":"Füzik, Tibor","last_name":"Füzik","first_name":"Tibor"},{"first_name":"Růžena","full_name":" Píchalová, Růžena","last_name":"Píchalová"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0003-4790-8078","full_name":"Florian Schur","last_name":"Schur"},{"first_name":"Karolína","last_name":"Strohalmová","full_name":"Strohalmová, Karolína"},{"full_name":"Křížová, Ivana","last_name":"Křížová","first_name":"Ivana"},{"last_name":"Hadravová","full_name":"Hadravová, Romana","first_name":"Romana"},{"last_name":"Rumlová","full_name":"Rumlová, Michaela","first_name":"Michaela"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John A"},{"first_name":"Pavel","full_name":"Ulbrich, Pavel","last_name":"Ulbrich"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"}],"date_updated":"2021-01-12T08:17:03Z","title":"Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging","month":"05","extern":1,"type":"journal_article","citation":{"ama":"Füzik T, Píchalová R, Schur FK, et al. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. 2016;90(9):4593-4603. doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>","chicago":"Füzik, Tibor, Růžena Píchalová, Florian KM Schur, Karolína Strohalmová, Ivana Křížová, Romana Hadravová, Michaela Rumlová, John Briggs, Pavel Ulbrich, and Tomáš Ruml. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>. ASM, 2016. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>.","ista":"Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová M, Briggs J, Ulbrich P, Ruml T. 2016. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. Journal of Virology. 90(9), 4593–4603.","mla":"Füzik, Tibor, et al. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>, vol. 90, no. 9, ASM, 2016, pp. 4593–603, doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>.","short":"T. Füzik, R. Píchalová, F.K. Schur, K. Strohalmová, I. Křížová, R. Hadravová, M. Rumlová, J. Briggs, P. Ulbrich, T. Ruml, Journal of Virology 90 (2016) 4593–4603.","apa":"Füzik, T., Píchalová, R., Schur, F. K., Strohalmová, K., Křížová, I., Hadravová, R., … Ruml, T. (2016). Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>","ieee":"T. Füzik <i>et al.</i>, “Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging,” <i>Journal of Virology</i>, vol. 90, no. 9. ASM, pp. 4593–4603, 2016."},"quality_controlled":0,"intvolume":"        90","acknowledgement":"Work in the laboratory of John A. G. Briggs was funded by Deutsche\nForschungsgemeinschaft (DFG) (BR 3635/2-1). This work, including the\nefforts of Tomas Ruml, was funded by the Grant Agency of the Czech\nRepublic (14-15326S) and the Czech Ministry of Education (NPU I sus-\ntainability projects LO1302 and LO1304).","issue":"9","publist_id":"6835","volume":90,"publication_status":"published","abstract":[{"lang":"eng","text":"The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle."}],"status":"public"},{"page":"506 - 508","doi":"10.1126/science.aaf9620","publication":"Science","day":"29","date_created":"2018-12-11T11:48:39Z","_id":"816","publisher":"American Association for the Advancement of Science","month":"07","date_updated":"2021-01-12T08:17:12Z","title":"An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation","year":"2016","author":[{"last_name":"Schur","full_name":"Florian Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"last_name":"Obr","full_name":"Martin Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wim","full_name":"Hagen, Wim J","last_name":"Hagen"},{"full_name":"Wan, William","last_name":"Wan","first_name":"William"},{"full_name":"Jakobi, Arjen J","last_name":"Jakobi","first_name":"Arjen"},{"full_name":"Kirkpatrick, Joanna M","last_name":"Kirkpatrick","first_name":"Joanna"},{"last_name":"Sachse","full_name":"Sachse, Carsten","first_name":"Carsten"},{"full_name":"Kraüsslich, Hans Georg","last_name":"Kraüsslich","first_name":"Hans"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John A"}],"date_published":"2016-07-29T00:00:00Z","extern":1,"type":"journal_article","citation":{"chicago":"Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>.","ama":"Schur FK, Obr M, Hagen W, et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. <i>Science</i>. 2016;353(6298):506-508. doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>","mla":"Schur, Florian KM, et al. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” <i>Science</i>, vol. 353, no. 6298, American Association for the Advancement of Science, 2016, pp. 506–08, doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>.","ista":"Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science. 353(6298), 506–508.","short":"F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse, H. Kraüsslich, J. Briggs, Science 353 (2016) 506–508.","apa":"Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs, J. (2016). An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>","ieee":"F. K. Schur <i>et al.</i>, “An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation,” <i>Science</i>, vol. 353, no. 6298. American Association for the Advancement of Science, pp. 506–508, 2016."},"status":"public","publist_id":"6834","volume":353,"abstract":[{"lang":"eng","text":"Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs.We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- And intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1."}],"publication_status":"published","intvolume":"       353","acknowledgement":"The authors thank B. Glass for preparation of the immature HIV-1 (D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory (EMBL) and from the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND (PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically supported by the EMBL information technology services unit and the EMBL Proteomics Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S. and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J., and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S. and J.A.G.B. wrote the manuscript with support from all authors. Representative tomograms and the final electron microscopy structures have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017, EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited in the Protein Data Bank with accession number 5L93.","issue":"6298","quality_controlled":0},{"scopus_import":1,"acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","oa":1,"intvolume":"        25","volume":25,"related_material":{"record":[{"id":"2940","status":"public","relation":"earlier_version"}]},"_id":"1479","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"}],"date_created":"2018-12-11T11:52:16Z","file_date_updated":"2020-07-14T12:44:56Z","pubrep_id":"766","publication":"Computational Complexity","page":"567 - 605","date_published":"2016-09-01T00:00:00Z","ec_funded":1,"date_updated":"2023-02-23T11:05:09Z","title":"A counterexample to the chain rule for conditional HILL entropy","month":"09","ddc":["004"],"file":[{"access_level":"open_access","file_name":"IST-2017-766-v1+1_678.pdf","date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf","file_size":483258,"relation":"main_file","checksum":"7659296174fa75f5f0364f31f46f4bcf","creator":"system","date_created":"2018-12-12T10:13:29Z","file_id":"5012"}],"type":"journal_article","citation":{"ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. 2016;25(3):567-605. doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>.","mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>.","ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., &#38; Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. Springer. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” <i>Computational Complexity</i>, vol. 25, no. 3. Springer, pp. 567–605, 2016."},"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.","lang":"eng"}],"publist_id":"5715","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publisher":"Springer","day":"01","doi":"10.1007/s00037-015-0120-9","oa_version":"Submitted Version","author":[{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","orcid":"0000-0003-2835-9093","full_name":"Krenn, Stephan","last_name":"Krenn"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Akshay","full_name":"Wadia, Akshay","last_name":"Wadia"},{"first_name":"Daniel","full_name":"Wichs, Daniel","last_name":"Wichs"}],"year":"2016","department":[{"_id":"KrPi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"year":"2016","author":[{"last_name":"Michałek","full_name":"Michałek, Mateusz","first_name":"Mateusz"},{"full_name":"Sturmfels, Bernd","last_name":"Sturmfels","first_name":"Bernd"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"first_name":"Piotr","full_name":"Zwiernik, Piotr","last_name":"Zwiernik"}],"date_published":"2016-01-07T00:00:00Z","month":"01","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:51:02Z","title":"Exponential varieties","day":"07","date_created":"2018-12-11T11:52:16Z","publisher":"Oxford University Press","_id":"1480","page":"27 - 56","oa_version":"Preprint","publication":"Proceedings of the London Mathematical Society","doi":"10.1112/plms/pdv066","intvolume":"       112","oa":1,"issue":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"5714","main_file_link":[{"url":"http://arxiv.org/abs/1412.6185","open_access":"1"}],"publication_status":"published","volume":112,"abstract":[{"lang":"eng","text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. "}],"scopus_import":1,"citation":{"ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","apa":"Michałek, M., Sturmfels, B., Uhler, C., &#38; Zwiernik, P. (2016). Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>.","ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. 2016;112(1):27-56. doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>"},"type":"journal_article"},{"type":"journal_article","citation":{"ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” <i>PLoS One</i>, vol. 11, no. 2. Public Library of Science, 2016.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","apa":"Adibi, M., Yoshida, S., Weijers, D., &#38; Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>.","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. 2016;11(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>"},"file":[{"date_created":"2018-12-12T10:14:16Z","creator":"system","file_id":"5066","access_level":"open_access","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","file_size":4297148,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","relation":"main_file","checksum":"6066146e527335030f83aa5924ab72a6"}],"ddc":["570"],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"5711","abstract":[{"text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","doi":"10.1371/journal.pone.0147830","day":"01","publisher":"Public Library of Science","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JiFr"}],"year":"2016","author":[{"full_name":"Adibi, Milad","last_name":"Adibi","first_name":"Milad"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Christian","last_name":"Fleck","full_name":"Fleck, Christian"}],"scopus_import":1,"volume":11,"oa":1,"intvolume":"        11","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","issue":"2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e0147830","publication":"PLoS One","pubrep_id":"521","file_date_updated":"2020-07-14T12:44:57Z","date_created":"2018-12-11T11:52:17Z","_id":"1482","month":"02","date_updated":"2021-01-12T06:51:03Z","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","date_published":"2016-02-01T00:00:00Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","issue":"6","intvolume":"        26","oa":1,"volume":26,"scopus_import":1,"date_published":"2016-06-01T00:00:00Z","date_updated":"2021-01-12T06:51:04Z","title":"Environmental and endogenous control of cortical microtubule orientation","month":"06","_id":"1484","date_created":"2018-12-11T11:52:17Z","pubrep_id":"1002","file_date_updated":"2020-07-14T12:44:57Z","publication":"Trends in Cell Biology","page":"409 - 419","quality_controlled":"1","publication_status":"published","publist_id":"5704","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","ddc":["581"],"article_type":"review","file":[{"access_level":"open_access","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","file_size":2329117,"relation":"main_file","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","date_created":"2018-12-12T10:15:34Z","creator":"system","file_id":"5155"}],"type":"journal_article","citation":{"ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” <i>Trends in Cell Biology</i>, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","apa":"Chen, X., Wu, S., Liu, Z., &#38; Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>.","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. 2016;26(6):409-419. doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>"},"author":[{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shuang","full_name":"Wu, Shuang","last_name":"Wu"},{"first_name":"Zengyu","last_name":"Liu","full_name":"Liu, Zengyu"},{"first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","last_name":"Friml"}],"year":"2016","department":[{"_id":"JiFr"}],"publisher":"Cell Press","day":"01","doi":"10.1016/j.tcb.2016.02.003","oa_version":"Submitted Version"},{"oa_version":"Preprint","doi":"10.1088/1478-3975/13/1/016003","day":"29","publisher":"IOP Publishing Ltd.","department":[{"_id":"GaTk"}],"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"year":"2016","type":"journal_article","citation":{"ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>.","ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. 2016;13(1). doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>","chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>.","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” <i>Physical Biology</i>, vol. 13, no. 1. IOP Publishing Ltd., 2016.","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>","short":"D. De Martino, Physical Biology 13 (2016)."},"language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.","lang":"eng"}],"publication_status":"published","publist_id":"5702","quality_controlled":"1","publication":"Physical Biology","date_created":"2018-12-11T11:52:18Z","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"_id":"1485","month":"01","date_updated":"2021-01-12T06:51:04Z","title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","ec_funded":1,"date_published":"2016-01-29T00:00:00Z","scopus_import":1,"volume":13,"main_file_link":[{"url":"http://arxiv.org/abs/1505.04613","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"1","intvolume":"        13","oa":1,"article_number":"016003"},{"quality_controlled":"1","article_number":"021101","oa":1,"intvolume":"        57","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1511.01995"}],"publist_id":"5701","publication_status":"published","volume":57,"abstract":[{"lang":"eng","text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime."}],"status":"public","language":[{"iso":"eng"}],"citation":{"ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2. American Institute of Physics, 2016.","apa":"Hainzl, C., &#38; Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>","short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>.","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.","chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>.","ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. 2016;57(2). doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>"},"scopus_import":1,"type":"journal_article","year":"2016","author":[{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"date_published":"2016-02-24T00:00:00Z","department":[{"_id":"RoSe"}],"title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","date_updated":"2021-01-12T06:51:04Z","month":"02","publisher":"American Institute of Physics","_id":"1486","day":"24","date_created":"2018-12-11T11:52:18Z","doi":"10.1063/1.4941723","publication":"Journal of Mathematical Physics","oa_version":"Preprint"}]