A graphical method to construct a phylogenetic tree

A 3D graphical representation of DNA sequences, which has no circuit or degeneracy, is derived for mathematical denotation of DNA sequence. Based on this graphical representation, we propose a new sequence distance measure. We make use of the corresponding similarity matrix to construct a phylogenic tree by virtue of the fuzzy theory. The examination of phylogenic tree belong to eight species illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

The assessment of compliance with legal limits. Part 2. How to consider both type I and type II errors when working in the concentration domain

Considering the uncertainty of measurement when assessing compliance with reference values given in compositional specifications and statutory limits is still a controversial matter. In theory, assessing compliance requires considering both type I (false positive) and type II (false negative) errors. The more the concentration of the analyte in the sample under investigation is close to the allowed concentration limit, the more critical it is to consider both types of errors. This paper describes how this could be done. The matter is discussed in the light of the most recent literature information.     

The asymptotic equivalence of Bayes and maximum likelihood estimation

Let (X, $\text{A}$) be a measurable space, Θ ? $\text{R}$ an open interval and P_Ω ∥ $\text{A}$, Ω ? Θ, a family of probability measures fulfilling certain regularity conditions. Let $\text{Ω}{}_{\mathrm{n}}$ be the maximum likelihood estimate for the sample size n. Let λ be a prior distribution on Θ and let $\text{R}{}_{\mathrm{<mtext>n,</mtext><mtext>x</mtext>}}$ be the posterior distribution for the sample size n given $\text{x}\text{? X}{}^{\mathrm{n}}$. $\text{L:}\text{Θ}\text{× Θ →}\text{R}$ denotes a loss function fulfilling certain regularity conditions and T_n denotes the Bayes estimate relative to λ and L for the sample size n. It is proved that for every compact K ? Θ there exists c_K ≥ 0 such that

This theorem improves results of Bickel and Yahav [3], and Ibragimov and Has'minskii [4], as far as the speed of convergence is concerned.     

A finite volume cell‐centered Lagrangian hydrodynamics approach for solids in general unstructured grids

A finite volume cell‐centered Lagrangian hydrodynamics approach, formulated in Cartesian frame, is presented for solving elasto‐plastic response of solids in general unstructured grids. Because solid materials can sustain significant shear deformation, evolution equations for stress and strain fields are solved in addition to mass, momentum, and energy conservation laws. The total stress is split into deviatoric shear stress and dilatational components. The dilatational response of the material is modeled using the Mie‐Grüneisen equation of state. A predicted trial elastic deviatoric stress state is evolved assuming a pure elastic deformation in accordance with the hypo‐elastic stress‐strain relation. The evolution equations are advanced in time by constructing vertex velocity and corner traction force vectors using multi‐dimensional Riemann solutions erected at mesh vertices. Conservation of momentum and total energy along with the increase in entropy principle are invoked for computing these quantities at the vertices. Final state of deviatoric stress is effected via radial return algorithm based on the J‐2 von Mises yield condition. The scheme presented in this work is second‐order accurate both in space and time. The suitability of the scheme is evinced by solving one‐ and two‐dimensional benchmark problems both in structured grids and in unstructured grids with polygonal cells. Copyright © 2013 John Wiley & Sons, Ltd.     

On clique relaxation models in network analysis

Increasing interest in studying community structures, or clusters in complex networks arising in various applications has led to a large and diverse body of literature introducing numerous graph-theoretic models relaxing certain characteristics of the classical clique concept. This paper analyzes the elementary clique-defining properties implicitly exploited in the available clique relaxation models and proposes a taxonomic framework that not only allows to classify the existing models in a systematic fashion, but also yields new clique relaxations of potential practical interest. Some basic structural properties of several of the considered models are identified that may facilitate the choice of methods for solving the corresponding optimization problems. In addition, bounds describing the cohesiveness properties of different clique relaxation structures are established, and practical implications of choosing one model over another are discussed.     

Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Maximum likelihood estimation for second level fMRI data analysis with expectation trust region algorithm

The trust region method which originated from the Levenberg–Marquardt (LM) algorithm for mixed effect model estimation are considered in the context of second level functional magnetic resonance imaging (fMRI) data analysis. We first present the mathematical and optimization details of the method for the mixed effect model analysis, then we compare the proposed methods with the conventional expectation-maximization (EM) algorithm based on a series of datasets (synthetic and real human fMRI datasets). From simulation studies, we found a higher damping factor for the LM algorithm is better than lower damping factor for the fMRI data analysis. More importantly, in most cases, the expectation trust region algorithm is superior to the EM algorithm in terms of accuracy if the random effect variance is large. We also compare these algorithms on real human datasets which comprise repeated measures of fMRI in phased-encoded and random block experiment designs. We observed that the proposed method is faster in computation and robust to Gaussian noise for the fMRI analysis. The advantages and limitations of the suggested methods are discussed.     

Equilibrium analysis for a mass-conserving model in presence of cavitation

We study the existence of equilibrium positions for the load problem in Lubrication Theory. The problem consists of two surfaces in relative motion separated by a small distance filled by a lubricant. The system is described by the modified Reynolds equation (Elrod–Adams model) which describes the behavior of the lubricant and an extra integral equation given the balance of forces. The balance of forces allows to obtain the unknown position of the surfaces, defined with one degree of freedom.     

Efficient one‐pot synthesis of water‐compatible and photoresponsive molecularly imprinted polymer nanoparticles by facile RAFT precipitation polymerization

A facile, general, and highly efficient one‐pot approach to obtain azobenzene (azo)‐containing molecularly imprinted polymer (MIP) nanoparticles with photoresponsive template binding and release properties in aqueous media is described, which involves the combined use of hydrophilic macromolecular chain transfer agent‐mediated reversible addition‐fragmentation chain transfer precipitation polymerization and easily available water‐insoluble azo functional monomers. The resulting azo‐containing MIPs were characterized with dynamic laser scattering (DLS), SEM, FTIR, static contact angle and water dispersion studies, and equilibrium binding experiments. They have proven to be nanoparticles (their diameters being around 104–397 nm, as determined by DLS in methanol) with surface‐grafted hydrophilic polymer brushes and exhibit excellent pure water‐compatible template binding properties. Moreover, obvious photoregulated template binding behaviors were observed for such azo‐containing MIP nanoparticles, which led to their largely accelerated template release in the aqueous media under the UV light irradiation. Furthermore, the general applicability of the strategy was also demonstrated. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1941–1952     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .