PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences

Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. Here, we present an online implementation of that alignment algorithm based on such probabilities. Our server takes as input a query RNA sequence and a large genome sequence, and outputs a list of hits that are above a mean posterior probability threshold. The output is presented in a format suited to local alignment. It can also be viewed within the PLAST alignment viewer applet that provides a list of all hits found and highlights regions of high posterior probability within each local alignment. The server is freely available at http://plastrna.njit.edu

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

BACKGROUND: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. FINDINGS: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8

Linear and nonlinear analysis of normal and CAD-affected heart rate signals

Coronary Artery Disease (CAD) is one of the dangerous cardiac disease, often may lead to sudden cardiac death. It is difficult to diagnose CAD by manual inspection of electrocardiogram (ECG) signals. To automate this detection task, in this study, we extracted the Heart Rate (HR) from the ECG signals and used them as base signal for further analysis. We then analyzed the HR signals of both normal and CAD subjects using (i) time domain, (ii) frequency domain and (iii) nonlinear techniques. The following are the nonlinear methods that were used in this work: Poincare plots, Recurrence Quantification Analysis (RQA) parameters, Shannon entropy, Approximate Entropy (ApEn), Sample Entropy (SampEn), Higher Order Spectra (HOS) methods, Detrended Fluctuation Analysis (DFA), Empirical Mode Decomposition (EMD), Cumulants, and Correlation Dimension. As a result of the analysis, we present unique recurrence, Poincare and HOS plots for normal and CAD subjects. We have also observed significant variations in the range of these features with respect to normal and CAD classes, and have presented the same in this paper. We found that the RQA parameters were higher for CAD subjects indicating more rhythm. Since the activity of CAD subjects is less, similar signal patterns repeat more frequently compared to the normal subjects. The entropy based parameters, ApEn and SampEn, are lower for CAD subjects indicating lower entropy (less activity due to impairment) for CAD. Almost all HOS parameters showed higher values for the CAD group, indicating the presence of higher frequency content in the CAD signals. Thus, our study provides a deep insight into how such nonlinear features could be exploited to effectively and reliably detect the presence of CAD

Carrier relaxation in GaAs v-groove quantum wires and the effects of localization

Carrier relaxation processes have been investigated in GaAs/AlGaAs v-groove quantum wires (QWRs) with a large subband separation (46 meV). Signatures of inhibited carrier relaxation mechanisms are seen in temperature-dependent photoluminescence (PL) and photoluminescence-excitation (PLE) measurements; we observe strong emission from the first excited state of the QWR below ~50 K. This is attributed to reduced inter-subband relaxation via phonon scattering between localized states. Theoretical calculations and experimental results indicate that the pinch-off regions, which provide additional two-dimensional confinement for the QWR structure, have a blocking effect on relaxation mechanisms for certain structures within the v-groove. Time-resolved PL measurements show that efficient carrier relaxation from excited QWR states into the ground state, occurs only at temperatures > 30 K. Values for the low temperature radiative lifetimes of the ground- and first excited-state excitons have been obtained (340 ps and 160 ps respectively), and their corresponding localization lengths along the wire estimated.Comment: 9 pages, 8 figures, submitted to Phys. Rev. B Attempted to correct corrupt figure

Bianchi Type I Cosmology in Generalized Saez-Ballester Theory via Noether Gauge Symmetry

In this paper, we investigate the generalized Saez-Ballester scalar-tensor theory of gravity via Noether gauge symmetry (NGS) in the background of Bianchi type I cosmological spacetime. We start with the Lagrangian of our model and calculate its gauge symmetries and corresponding invariant quantities. We obtain the potential function for the scalar field in the exponential form. For all the symmetries obtained, we determine the gauge functions corresponding to each gauge symmmetry which include constant and dynamic gauge. We discuss cosmological implications of our model and show that it is compatible with the observational data.Comment: 13 pages, 2 figures, accepted for publication in 'European Physical Journal C