An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels

We propose a suite of novel algorithms for image analysis of protein expression images obtained from 2-D electrophoresis. These algorithms are a segmentation algorithm for protein spot identification, and an algorithm for matching protein spots from two corresponding images for differential expression study. The proposed segmentation algorithm employs the watershed transformation, k-means analysis, and distance transform to locate the centroids and to extract the regions of the proteins spots. The proposed spot matching algorithm is an integration of the hierarchical-based and optimization-based methods. The hierarchical method is first used to find corresponding pairs of protein spots satisfying the local cross-correlation and overlapping constraints. The matching energy function based on local structure similarity, image similarity, and spatial constraints is then formulated and optimized. Our new algorithm suite has been extensively tested on synthetic and actual 2-D gel images from various biological experiments, and in quantitative comparisons with ImageMaster2D Platinum the proposed algorithms exhibit better spot detection and spot matching.     

Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.     

Monovalent cation localization in DNA A-tracts with different sequences

The free solution mobilities of 26-base pair (bp) DNA oligomers containing A-tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26-bp random-sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li⁺ and tetrapropylammonium (TPA⁺) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA⁺, indicating that the A-tract and reference oligomers had the same B-form conformation in this BGE. With increasing [Li⁺], the mobility ratio decreased as Li⁺ ions became localized in the A-tract minor groove, suggesting that the A-tract was now in the B* conformation. If the A-tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li⁺] increased to 0.3 M. However, for A-tracts without an internal ApT step and for A-tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li⁺], eventually reaching a plateau value of 1.00. Hence, DNA A-tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li⁺], the A-tract sequence, and the total A + T content of the oligomer.     

Localization of the eigenvalues of a pencil of positive definite matrices

Let A and B be real square positive definite matrices close to each other. A domain S on the complex plane that contains all the eigenvalues λ of the problem Az = λBz is constructed analytically. The boundary ?S of S is a curve known as the limacon of Pascal. Using the standard conformal mapping of the exterior of this curve (or of the exterior of an enveloping circular lune) onto the exterior of the unit disc, new analytical bounds are obtained for the convergence rate of the minimal residual method (GMRES) as applied to solving the linear system Ax = b with the preconditioner B.     

Quantification of the pore size distribution (porosity profiles) in microfiltration membranes by SEM,TEM and computer image analysis

Transport properties of membranes are closely related to morphological properties like surface porosity and variation of their inner pore structure. Scanning electron microscopy (SEM) as well as transmission electron microscopy (TEM) are powerful tools to characterise the microscopical pore structure of membranes in a qualitative manner. In order to provide more quantitative data of surface and cross-sectional pores computer image analysis can be used. Parameters like ‘porous area fraction’ and ‘mean free path length’ have been selected to describe the pore distribution within porosity profiles in order to consider the effect that the pores within the cross-section are connected to each other.     

Effect of sound wave stress on antioxidant enzyme activities and lipid peroxidation of Dendrobium candidum

The effect of sound wave stress on important medicinal plant, Dendrobium candidum Wall. ex Lindl, was investigated, including the responses on malondialdehyde (MDA) content, the activities change of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX). Results were found that the activities of SOD, CAT, POD and APX enhanced totally in different organs of D. candidum, as leaves, stems and roots, in response to the stress. Furthermore there happened similar shift of antioxidant enzymes activities, which increased in the initial stimulation and decreased afterwards. Data showed SOD, CAT, POD and APX activities ascended to max at day 9, 6, 9 and 12 in leaves, at day 9, 6, 12 and 9 in stems, and at day 12, 6, 9 and 9 in roots, respectively. As a lipid peroxidation parameter, MDA content in different organs increased in the beginning, dropped afterward, and increased again in the late. Anyway the total trend was the rise of MDA level compared to the control. It was interesting that the MDA content appeared the lowest levels almost when the antioxidant enzymes activities were up to the highest. Our results demonstrated the different organs of D. candidum might produce accumulation of active oxygen species (AOS) under initial treatment of sound wave stress. Later AOS might start to reduce due to the enhancement of antioxidant enzymes activities treated by the stress. The data revealed that the antioxidant metabolism was to be important in determining the ability of plants to survive in sound stress, and the up regulation of these enzymes activities would help to reduce the build up of AOS, which could protect plant cells from oxidative damage. Moreover, different cell compartments might activate different defensive system to reduce excessive amount of AOS. Finally the mechanism of this action was also discussed simply.     

Evaluation of image sticking property on liquid crystal displays with polymer layers produced from phenanthrene-carrying monomers

As a model of polymer-sustained-alignment liquid crystal display (PSA-LCD), the liquid crystal (LC) cells having the polymer layers produced from monomers of phenanthrene (Phen)-carrying monomers, 2,7-, 3,8-, 1,8- and 3,6-dimethacryloyl-oxy-phenanthrene (DMAPhen), were prepared and investigated image sticking phenomenon with evaluations of residual direct current voltage (V_rDC) and difference in pretilt angle before and after application of alternate current voltage (Δtilt). The V_rDC values were small for the LC cells with the polymer layers produced from the Phen-carrying monomers used in this study. On the other hand, Δtilt depends on the molecular structure of the Phen-carrying monomer. The Δtilt values became small with increasing the linearity of the monomer structure for the Phen-carrying monomers. The findings would be useful for obtaining the small level of image sticking in the PSA-LCDs produced from the Phen-carrying monomers.     

The H2+ molecular ion: Low-lying states

Matching for a wavefunction the WKB expansion at large distances and Taylor expansion at small distances leads to a compact, few-parametric uniform approximation found in Turbiner and Olivares-Pilon (2011). The ten low-lying eigenstates of H₂⁺ of the quantum numbers (n,m,Λ,±)$(n,m,\Lambda ,\pm )$  with n=m=0$n=m=0$ at Λ=0,1,2$\Lambda =0,1,2$, with n=1$n=1$, m=0$m=0$ and n=0$n=0$, m=1$m=1$ at Λ=0$\Lambda =0$ of both parities are explored for all interproton distances R$R$. For all these states this approximation provides the relative accuracy ?10⁻⁵$?10^{-5}$ (not less than 5 s.d.) locally, for any real coordinate x$x$ in eigenfunctions, when for total energy E(R)$E\left(R\right)$ it gives 10-11 s.d. for R∈[0,50]$R\in [0,50]$  a.u. Corrections to the approximation are evaluated in the specially-designed, convergent perturbation theory. Separation constants are found with not less than 8 s.d. The oscillator strength for the electric dipole transitions E1$E1$ is calculated with not less than 6 s.d. A dramatic dip in the E1$E1$ oscillator strength f_{1sσg−3pσu}$f_{1s{\sigma }_g-3p{\sigma }_u}$ at R∼R_eq$R\sim R_{eq}$ is observed. The magnetic dipole and electric quadrupole transitions are calculated for the first time with not less than 6 s.d. in oscillator strength. For two lowest states (0,0,0,±)$(0,0,0,\pm )$ (or, equivalently, 1sσ_g$1s{\sigma }_g$ and 2pσ_u$2p{\sigma }_u$ states) the potential curves are checked and confirmed in the Lagrange mesh method within 12 s.d. Based on them the Energy Gap between 1sσ_g$1s{\sigma }_g$ and 2pσ_u$2p{\sigma }_u$ potential curves is approximated with modified Pade Re^−R[Pade(8/7)](R)$R{e}^{-R}\left[Pade(8/7)\right]\left(R\right)$ with not less than 4-5 figures at R∈[0,40]$R\in [0,40]$ a.u. Sum of potential curves E_1sσg+E_2pσu$E_{1s{\sigma }_g}+E_{2p{\sigma }_u}$ is approximated by Pade 1/R[Pade(5/8)](R)$1/R\left[Pade(5/8)\right]\left(R\right)$ in R∈[0,40]$R\in [0,40]$ a.u. with not less than 3-4 figures.     

The modelling of desk screens by a combined BEM – Source image approach

An original BEM approach is proposed to study the efficiency of desk screens in open plan offices. For large offices the volume geometry can be approximated by two horizontal planes – for floor and ceiling – and the source image approach is used to compute an approximated room Green function. When used in combination with the BEM approach, this allows reducing the discretised boundary to the desks only. The computation of the room Green functions is based on the modelling of the floor and ceiling response by means of the image source approach. The proposed approach is validated both numerically and experimentally. Very significant reductions of computation times have been obtained. The approach is used in an attempt to design efficient desk screens.