Patterns and influencing factor of synonymous codon usage in porcine circovirus

<p>Abstract</p> <p>Background</p> <p>Analysis of codon usage can reveal much about the molecular evolution of the viruses. Nevertheless, little information about synonymous codon usage pattern of porcine circovirus (PCV) genome in the process of its evolution is available. In this study, to give a new understanding on the evolutionary characteristics of PCV and the effects of natural selection from its host on the codon usage pattern of the virus, Patterns and the key determinants of codon usage in PCV were examined.</p> <p>Methods</p> <p>We carried out comprehensive analysis on codon usage pattern in the PCV genome, by calculating relative synonymous codon usage (RSCU), effective number of codons (ENC), dinucleotides and nucleic acid content of the PCV genome.</p> <p>Results</p> <p>PCV genomes have relatively much lower content of GC and codon preference, this result shows that nucleotide constraints have a major impact on its synonymous codon usage. The results of the correspondence analysis indicate codon usage patterns of PCV of various genotypes, various subgenotypes changed greatly, and significant differences in codon usage patterns of Each virus of Circoviridae.There is much comparability between PCV and its host in their synonymous codon usage, suggesting that the natural selection pressure from the host factor also affect the codon usage patterns of PCV. In particular, PCV genotype II is in synonymous codon usage more similar to pig than to PCV genotype I, which may be one of the most important molecular mechanisms of PCV genotype II to cause disease. The calculations results of the relative abundance of dinucleotides indicate that the composition of dinucleotides also plays a key role in the variation found in synonymous codon usage in PCV. Furthermore, geographic factors, the general average hydrophobicity and the aromaticity may be related to the formation of codon usage patterns of PCV.</p> <p>Conclusion</p> <p>The results of these studies suggest that synonymous codon usage pattern of PCV genome are the result of interaction between mutation pressure and natural selection from its host. The information from this study may not only have theoretical value in understanding the characteristics of synonymous codon usage in PCV genomes, but also have significant value for the molecular evolution of PCV.</p

Signature of the γ\gamma+jet and dijet production mediated by an excited quark with QCD next-to-leading order accuracy at the LHC

We present a detailed study of the production and decay of the excited quark at the QCD next-to-leading order (NLO) level at the Large Hadron Collider, using the narrow width approximation and helicity amplitudes method. We find that the QCD NLO corrections can tighten the constraints on the model parameters and reduce the scale dependencies of the total cross sections. We discuss the signals of the excited quark production with decay mode $q^{\ast}\rightarrow q\gamma$ and $q^{\ast}\rightarrow qg$, and present several important kinematic distributions. Moreover, we give the upper limits of the excited quark excluded mass range and the allowed parameter space for the coupling constants and the excited quark mass.Comment: 20 pages, 13 figures; version published in PR

Understanding the Generalization Performance of Spectral Clustering Algorithms

The theoretical analysis of spectral clustering mainly focuses on consistency, while there is relatively little research on its generalization performance. In this paper, we study the excess risk bounds of the popular spectral clustering algorithms: \emph{relaxed} RatioCut and \emph{relaxed} NCut. Firstly, we show that their excess risk bounds between the empirical continuous optimal solution and the population-level continuous optimal solution have a $\mathcal{O}(1/\sqrt{n})$ convergence rate, where $n$ is the sample size. Secondly, we show the fundamental quantity in influencing the excess risk between the empirical discrete optimal solution and the population-level discrete optimal solution. At the empirical level, algorithms can be designed to reduce this quantity. Based on our theoretical analysis, we propose two novel algorithms that can not only penalize this quantity, but also cluster the out-of-sample data without re-eigendecomposition on the overall sample. Experiments verify the effectiveness of the proposed algorithms

Transverse momentum resummation for color sextet and antitriplet scalar production at the LHC

We study the factorization and resummation of the transverse momentum spectrum of the color sextet and antitriplet scalars produced at the LHC based on soft-collinear effective theory. Compared to Z boson and Higgs production, a soft function is required to account for the soft gluon emission from the final-state colored scalar. The soft function is calculated at the next-to-leading order, and the resummation is performed at the approximate next-to-next-to-leading logarithmic accuracy. The non-perturbative effects and PDF uncertainties are also discussed.Comment: 20 pages, 7 figure