Numerical encoding plays an important role in DNA sequence analysis via computational methods, in which numerical values are associated with corresponding symbolic characters. After numerical representation, digital signal processing methods can be exploited to analyze DNA sequences. To reflect the biological properties of the original sequence, it is vital that the representation is one-to-one. Chaos Game Representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane that allows the depiction of the DNA sequence in the form of image. Using CGR, a biological sequence can be transformed one-to-one to a numerical sequence that preserves the main features of the original sequence. In this research, we propose to encode DNA sequences by considering 2D CGR coordinates as complex numbers, and apply digital signal processing methods to analyze their evolutionary relationship. Computational experiments indicate that this approach gives comparable results to the state-of-the-art multiple sequence alignment method, Clustal Omega, and is significantly faster. The MATLAB code for our method can be accessed from: www.mathworks.com/matlabcentral/fileexchange/57152
The entanglement quantification and classification of multipartite quantum states is an important research area in quantum information. In this paper, in terms of the reduced density matrices corresponding to all possible partitions of the entire system, a bounded entanglement measure is constructed for arbitrary-dimensional multipartite quantum states. In particular, for three-qubit quantum systems, we prove that our entanglement measure satisfies the relation of monogamy. Furthermore, we present a necessary condition for characterizing maximally entangled states using our entanglement measure.
Jianlian CuiDepartment of Mathematics, Tsinghua University,Chi-KwongLiDepartment of Mathematics, College of William and MaryNung-SingSzeDepartment of Applied Mathematics, The Hong Kong Polytechnic University
It is known that every complex square matrix with nonnega-tive determinant is the product of positive semi-definite matrices. There are characterizations of matrices that require two or five positive semi-definite matrices in the product. However, the characterizations of matrices that require three or four positive semi-definite matrices in the product are lacking. In this paper, we give a complete characterization of these two types of matrices. With these results, we give an algorithm to determine whether a square matrix can be expressed as the product of kpositive semi-definite matrices but not fewer, for k=1, 2, 3, 4, 5.
The free-living SAR11 clade is a globally abundant group of oceanic Alphaproteobacteria, with small genome sizes and rich genomic A+T content. However, the taxonomy of SAR11 has become controversial recently. Some researchers argue that the position of SAR11 is a sister group to Rickettsiales. Other researchers advocate that SAR11 is located within free-living lineages of Alphaproteobacteria. Here, we use the natural vector representation method to identify the evolutionary origin of the SAR11 clade. This alignment-free method does not depend on any model assumptions. With this approach, the correspondence between proteome sequences and their natural vectors is one-to-one. After fixing a set of proteins, each bacterium is represented by a set of vectors. The Hausdorff distance is then used to compute the dissimilarity distance between two bacteria. The phylogenetic tree can be reconstructed based on these distances. Using our method, we systematically analyze four data sets of alphaproteobacterial proteomes in order to reconstruct the phylogeny of Alphaproteobacteria. From this we can see that the phylogenetic position of the SAR11 group is within a group of other free-living lineages of Alphaproteobacteria.
JEFFREY MOOREUniversity of MarylandZHIHONG CHENGUniversity of MarylandJUNJIE HAOUniversity of MarylandGANG GUOThe Mennel Milling CompanyJian-Guo LiuUniversity of MarylandCHUNJIAN LINUniversity of MarylandLIANGLI (LUCY) YUUniversity of Maryland
Journal of Agricultural and Food Chemistry, 55, (25), 10173-10182, 2007.12
The bran fraction of wheat grain is known to contain significant quantities of bioactive components. This study evaluated the potential of solid-state yeast fermentation to improve the health beneficial properties of wheat bran, including extractable antioxidant properties, protein contents, and soluble and insoluble fiber compositions. Three commercial food grade yeast preparations were evaluated in the study along with the effects of yeast dose, treatment time, and their interaction with the beneficial components. Solid-state yeast treatments were able to significantly increase releasable antioxidant properties ranging from 28 to 65, from 0 to 20, from 13 to 19, from 0 to 25, from 50 to 100, and from 3 to 333% for scavenging capacities against peroxyl (ORAC), ABTS cation, DPPH and hydroxyl radicals, total phenolic contents (TPC), and phenolic acids, respectively. Yeast treatment increased protein content 11-12% but did not significantly alter the fiber composition of wheat bran. Effects of solid-state yeast treatment on both ORAC and TPC of wheat bran were altered by yeast dose, treatment time, and their interaction. Results suggest that solid-state yeast treatment may be a commercially viable postharvest procedure for improving the health beneficial properties of wheat bran and other wheat-based food ingredients.