Efficacy of different protein descriptors in predicting protein functional families

10.1186/1471-2105-8-300BMC Bioinformatics8-BBMI

Degeneracy in Candecomp/Parafac and Indscal Explained For Several Three-Sliced Arrays With A Two-Valued Typical Rank

The Candecomp/Parafac (CP) method decomposes a three-way array into a prespecified number R of rank-1 arrays, by minimizing the sum of squares of the residual array. The practical use of CP is sometimes complicated by the occurrence of so-called degenerate sequences of solutions, in which several rank-1 arrays become highly correlated in all three modes and some elements of the rank-1 arrays become arbitrarily large. We consider the real-valued CP decomposition of all known three-sliced arrays, i.e., of size p×q×3, with a two-valued typical rank. These are the 5×3×3 and 8×4×3 arrays, and the 3×3×4 and 3×3×5 arrays with symmetric 3×3 slices. In the latter two cases, CP is equivalent to the Indscal model. For a typical rank of {m,m+1}, we consider the CP decomposition with R=m of an array of rank m+1. We show that (in most cases) the CP objective function does not have a minimum but an infimum. Moreover, any sequence of feasible CP solutions in which the objective value approaches the infimum will become degenerate. We use the tools developed in Stegeman (2006), who considers p×p×2 arrays, and present a framework of analysis which is of use to the future study of CP degeneracy related to a two-valued typical rank. Moreover, our examples show that CP uniqueness is not necessary for degenerate solutions to occur

Theoretical study of the two-proton halo candidate 17^{17}Ne including contributions from resonant continuum and pairing correlations

With the relativistic Coulomb wave function boundary condition, the energies, widths and wave functions of the single proton resonant orbitals for $^{17}$Ne are studied by the analytical continuation of the coupling constant (ACCC) approach within the framework of the relativistic mean field (RMF) theory. Pairing correlations and contributions from the single-particle resonant orbitals in the continuum are taken into consideration by the resonant Bardeen-Cooper-Schrieffer (BCS) approach, in which constant pairing strength is used. It can be seen that the fully self-consistent calculations with NL3 and NLSH effective interactions mostly agree with the latest experimental measurements, such as binding energies, matter radii, charge radii and densities. The energy of $\pi$2s$_{1/2}$ orbital is slightly higher than that of $\pi1d_{5/2}$ orbital, and the occupation probability of the $(\pi$2s$_{1/2})^2$ orbital is about 20%, which are in accordance with the shell model calculation and three-body model estimation

Nonlinear wave transmission and pressure on the fixed truncated breakwater using NURBS numerical wave tank

Fully nonlinear wave interaction with a fixed breakwater is investigated in a numerical wave tank (NWT). The potential theory and high-order boundary element method are used to solve the boundary value problem. Time domain simulation by a mixed Eulerian-Lagrangian (MEL) formulation and high-order boundary integral method based on non uniform rational B-spline (NURBS) formulation is employed to solve the equations. At each time step, Laplace equation is solved in Eulerian frame and fully non-linear free-surface conditions are updated in Lagrangian manner through material node approach and fourth order Runge-Kutta time integration scheme. Incident wave is fed by specifying the normal flux of appropriate wave potential on the fixed inflow boundary. To ensure the open water condition and to reduce the reflected wave energy into the computational domain, two damping zones are provided on both ends of the numerical wave tank. The convergence and stability of the presented numerical procedure are examined and compared with the analytical solutions. Wave reflection and transmission of nonlinear waves with different steepness are investigated. Also, the calculation of wave load on the breakwater is evaluated by first and second order time derivatives of the potential

Multiwavelength studies of MHD waves in the solar chromosphere: An overview of recent results

The chromosphere is a thin layer of the solar atmosphere that bridges the relatively cool photosphere and the intensely heated transition region and corona. Compressible and incompressible waves propagating through the chromosphere can supply significant amounts of energy to the interface region and corona. In recent years an abundance of high-resolution observations from state-of-the-art facilities have provided new and exciting ways of disentangling the characteristics of oscillatory phenomena propagating through the dynamic chromosphere. Coupled with rapid advancements in magnetohydrodynamic wave theory, we are now in an ideal position to thoroughly investigate the role waves play in supplying energy to sustain chromospheric and coronal heating. Here, we review the recent progress made in characterising, categorising and interpreting oscillations manifesting in the solar chromosphere, with an impetus placed on their intrinsic energetics.Comment: 48 pages, 25 figures, accepted into Space Science Review

Early carboniferous brachiopod faunas from the Baoshan block, west Yunnan, southwest China

38 brachiopod species in 27 genera and subgenera are described from the Yudong Formation in the Shidian-Baoshan area, west Yunnan, southwest China. New taxa include two new subgenera: Unispirifer (Septimispirifer) and Brachythyrina (Longathyrina), and seven new species: Eomarginifera yunnanensis, Marginatia cylindrica, Unispirifer (Unispirifer) xiangshanensis, Unispirifer (Septimispirifer) wafangjieensis, Brachythyrina (Brachythyrina) transversa, Brachythyrina (Longathyrina) baoshanensis, and Girtyella wafangjieensis. Based on the described material and constraints from associated coral and conodont faunas, the age of the brachiopod fauna from the Yudon Formation is considered late Tournaisian (Early Carboniferous), with a possibility extending into earlyViseacutean.<br /

Effects of heat stress on the hepatic transcriptome of yellow-feathered chickens

Heat stress is one of the main environmental factors that hamper the efficiency of poultry production. Heat stress is known to be less harmful to yellow-feathered chickens (YFC) than to commercial broilers, especially in its effect on the relative weight of organs. The transcriptome was used to examine the gene expression profile of the livers of YFC that were exposed to heat stress. Mean liver weight (HW) and the hepatic weight index (HWI) of birds in the heat stress group did not differ significantly from those of the control group. A total of 596 genes were differentially expressed in the liver in response to heat stress. The enrichment results of differentially expressed genes (DEG) showed that many of these genes were related to the Fanconi anaemia pathway and that the cell cycle pathway was modulated. Thus, it can be concluded that these genes might be involved in improving the stability of the YFC liver genome and controlling the physiological response to heat stress. Keywords:, heat stress, liver, transcriptome, yellow-feathered chicken