A noise-resistant algorithm for grid finding in microarray image analysis

We present an algorithm for automatic spot localization for microarray images with rectangular spot and block packing. As an input, the algorithm requires only the common array design parameters: number of block rows and columns and number of spot rows and columns within each block. It proved to be robust with respect to different types of contamination and can tolerate a high percentage of the missing spots. The validity of the developed algorithm has been tested and confirmed using a large set of images of various designs from different microarray platforms. Comparison with academic and commercial packages has shown that for uncontaminated images our algorithm performs similarly, whereas for certain problematic images it outperforms the other packages.Patent pending.     

Superparamagnetic Nanostructures for Off‐Resonance Magnetic Resonance Spectroscopic Imaging

This study proposes a new method to generate positive contrast in magnetic resonance imaging (MRI) using superparamagnetic contrast agents. Superparamagnetic nanostructures consisting of octahedron manganese ferrite nanoparticles embedded in spherical nanogels are fabricated using a bottom‐up approach. The composite nanoparticles are strongly magnetized in an external magnetic field and produce a unique NMR frequency shift in water protons, which can be demonstrated in MR spectroscopy and imaging to be different from the bulk pool. Moreover, the particles exhibit excellent colloidal stability in aqueous media and good cell biocompatibility. Hence, these particles are potentially useful as biomarkers by taking advantage of the positive contrast effects produced in MRI.     

Existentially informed HIV-related psychotherapy.

This article describes an existentially informed approach to conducting psychotherapy with individuals living with the human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS). Uses of existential concepts to guide a holistic conceptualization of the individual and illuminate core existential concerns and dilemmas in confronting HIV-related challenges are delineated. Applications of existential ideas regarding psychotherapy process and technique in HIV-related psychotherapy also are illustrated. It is concluded that existential psychotherapy offers a conceptual framework that is especially well suited to the work of psychotherapy with individuals living with HIV disease, although the approach has received only limited attention in the HIV-related psychotherapy literature. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Is Protein Folding a Thermodynamically Unfavorable,Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.     

Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.     

Liquid salt cooled flexible conversion ratio fast reactor: Neutronic design

This paper presents the neutronic design of a liquid salt cooled fast reactor with flexible conversion ratio. The main objective of the design is to accommodate interchangeably within the same reactor core alternative transuranic actinides management strategies ranging from pure burning to self-sustainable breeding. Two, the most limiting, core design options with unity and zero conversion ratios are described. Ternary, NaCl-KCl-MgCl₂ salt was chosen as a coolant after a rigorous screening process, due to a combination of favourable neutronic and heat transport properties. Large positive coolant temperature reactivity coefficient was identified as the most significant design challenge. A wide range of strategies aiming at the reduction of the coolant temperature coefficient to assure self-controllability of the core in the most limiting unprotected accidents were explored. However, none of the strategies resulted in sufficient reduction of the coolant temperature coefficient without significantly compromising the core performance characteristics such as power density or cycle length. Therefore, reactivity control devices known as lithium thermal expansion modules were employed instead. This allowed achieving all the design goals for both zero and unity conversion ratio cores. The neutronic feasibility of both designs was demonstrated through calculation of reactivity control and fuel loading requirements, fluence limits, power peaking factors, and reactivity feedback coefficients.     

Large-eddy simulation of turbulent heat convection in a spanwise rotating channel flow

In this paper, we investigate the effects of the Coriolis force in a heated plane channel flow subjected to spanwise rotation using the method of large-eddy simulation. We present both the general and simplified transport equations for the resolved turbulent stresses, which are essential for understanding the unique pattern of turbulent kinetic energy production in a rotating system. Numerical simulations are performed using primarily two dynamic subgrid-scale stress models and one dynamic subgrid-scale heat flux model; namely, the conventional dynamic model (DM) and a novel dynamic nonlinear model (DNM) for closure of the filtered momentum equation, and an advanced dynamic full linear tensor thermal diffusivity model (DFLTDM) for closure of the filtered thermal energy equation. The turbulent flow field studied herein is characterized by a Reynolds number Re_τ = 150 and various rotation numbers Ro_τ ranging from 0 to 7.5. In order to validate the LES approach, turbulent statistics obtained from the simulations are thoroughly compared with the available experimental results and direct numerical simulation (DNS) data. A detailed comparative study has been conducted in order to evaluate the performance of the DM and DNM in terms of their prediction of characteristic features of the velocity and temperature fields and their capability of reflecting both forward and backward scatter of kinetic energy between the filtered and subgrid scales.