UPDG: Utilities package for data analysis of Pooled DNA GWAS

<p>Abstract</p> <p>Background</p> <p>Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).</p> <p>Results</p> <p>UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.</p> <p>Conclusions</p> <p>UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.</p

Ionospheric Effects on GPS Signal in Low-Latitude Region: A Case Study Review of South East Asia and Africa

The ionosphere is a significant source of errors affecting L-Band (1-2 GHz) signal propagation using Global Position System (GPS). The propagated GPS signals that passes through the Earth’s atmosphere where affected by ionosphere and troposphere irregularities and caused the signal propagation delay. However, the velocity of signals that propagate within the atmosphere deviates from vacuum line of sight (LOS), while the refractivity of ionosphere and troposphere influence the signal propagation delay causing atmospheric effects due to high electrons density.  Both affect the signal in different ways due to their particular refractive properties. The review focuses of some of the previous research studies conducted on empirical modeling of the ionospheric effect in low latitude region. The tabulated findings of such models presented in this article.http://dx.doi.org/10.4314/njt.v34i3.1

Perturbative Symmetry Approach

Perturbative Symmetry Approach is formulated in symbolic representation. Easily verifiable integrability conditions of a given equation are constructed in the frame of the approach. Generalisation for the case of non-local and non-evolution equations is disscused. Application of the theory to the Benjamin-Ono and Camassa-Holm type equations is considered.Comment: 16 page

X-ray radiation and runaway electron beams generated during discharges in atmospheric-pressure air at rise times of voltage pulse of 500 and 50 ns

The parameters of X-ray radiation and runaway electron beams (RAEBs) generated at long-pulse discharges in atmospheric-pressure air were investigated. In the experiments, high-voltage pulses with the rise times of 500 and 50 ns were applied to an interelectrode gap. The gap geometry provided non-uniform distribution of the electric field strength. It was founded that at the voltage pulse rise time of 500 ns and the maximum breakdown voltage Um for 1 cm-length gap, a duration [full width at half maximum (FWHM)] of a RAEB current pulse shrinks to 0.1 ns. A decrease in the breakdown voltage under conditions of a diffuse dischargeleads to an increase in the FWHM duration of the electron beam current pulse up to several nanoseconds. It was shown that when the rise time of the voltage pulse is of 500 ns and thediffuse discharge occurs in the gap, the FWHM duration of the X-ray radiation pulse canreach≈100 ns. It was established that at a pulse-periodic diffuse discharge fed by high-voltage pulses with the rise time of 50 ns, an energy of X-ray quanta and their number increase with increasing breakdown voltage. Wherein the parameter Um/pd is saved

Supershort avalanche electron beam in SF6 and krypton

Runaway electrons play an important role in the avalanche formation in nanosecond- and subnanosecond- pulse discharges. In this paper, characteristics of a supershort avalanche electron beam (SAEB) generated at the subnanosecond and nanosecond breakdown in sulfur hexafluoride (SF6 ) in an inhomogeneous electric field were studied. One pulser operated at negative polarity with voltage pulse amplitude of ˜130 kV and rise time of 0.3 ns. The other pulser operated at negative polarity with voltage pulse amplitude of 70 kV and rise time of ˜1.6 ns . SAEB parameters in SF6 are compared with those obtained in krypton (Kr), nitrogen (N2 ), air, and mixtures of SF6 with krypton or nitrogen. Experimental results showed that SAEB currents appeared during the rise-time of the voltage pulse for both pulsers. Moreover, amplitudes of the SAEB current in SF6 and Kr approximately ranged from several to tens of milliamps at atmospheric pressure, which were smaller than those in N2 and air (ranging from hundreds of milliamps to several amperes). Furthermore, the concentration of SF6 additive could significantly reduce the SAEB current in N2-SF6 mixture, but it slightly affected the SAEB current in Kr -SF6 mixture because of the atomic/molecular ionization cross section of the gas had a much greater impact on the SAEB current rather than the electronegativity

Review of supershort avalanche electron beam during nanosecond-pulse discharges in some gases

Supershort avalanche electron beam (SAEB) plays an important role in nanosecond-pulse discharges. This paper aims at reviewing experiments results on characteritics of SAEB and its spectra in different gases in nanosecond-pulse discharges. All the joint experiments were carried in the Institute of High Current Electronics of the Russian Academy of Sciences and the Institute of Electrical Engineering of the Chinese Academy of Sciences. In these experiments, the generation of a SAEB in SF6 in an inhomogeneous electric field was studied on three generators with pulse rise times of 0.3, 0.5 and ∼2 ns. Firstly, the comparison of SAEB parameters in SF6 with those obtained in other gases (air, nitrogen, argon, and krypton) is introduced. Secondly, the SAEB spectra in SF6 and air at pressures of 10 kPa (75 torr), and 0.1 MPa (750 torr) are reviewed and discussed. Finally, 1.5-D theoretical simulation of the supershort pulse of the fast electron beam in a coaxial diode filled with SF6 at atmospheric pressure is described. The simulation was carried out in the framework of hybrid model for discharge and runaway electron kinetics. The above research progress can provide better understanding of the investigation into the mechanism of nanosecond-pulse discharges

Enzyme‐assisted aqueous extraction of Kalahari melon seed oil: optimization using response surface methodology

Enzymatic extraction of oil from Kalahari melon seeds was investigated and evaluated by response surface methodology (RSM). Two commercial protease enzyme products were used separately: Neutrase® 0.8 L and Flavourzyme® 1000 L from Novozymes (Bagsvaerd, Denmark). RSM was applied to model and optimize the reaction conditions namely concentration of enzyme (20–50 g kg−1 of seed mass), initial pH of mixture (pH 5–9), incubation temperature (40–60 °C), and incubation time (12–36 h). Well fitting models were successfully established for both enzymes: Neutrase 0.8 L (R 2 = 0.9410) and Flavourzyme 1000 L (R 2 = 0.9574) through multiple linear regressions with backward elimination. Incubation time was the most significant reaction factor on oil yield for both enzymes. The optimal conditions for Neutrase 0.8 L were: an enzyme concentration of 25 g kg−1, an initial pH of 7, a temperature at 58 °C and an incubation time of 31 h with constant shaking at 100 rpm. Centrifuging the mixture at 8,000g for 20 min separated the oil with a recovery of 68.58 ± 3.39%. The optimal conditions for Flavourzyme 1000 L were enzyme concentration of 21 g kg−1, initial pH of 6, temperature at 50 °C and incubation time of 36 h. These optimum conditions yielded a 71.55 ± 1.28% oil recovery

Detection and Phylogenetic Analysis of Wolbachia in the Asiatic Rice Leafroller, Cnaphalocrocis medinalis, in Chinese Populations

Wolbachia are a group of intracellular inherited endosymbiontic bacteria infecting a wide range of insects. In this study the infection status of Wolbachia (Rickettsiales: Rickettsiaceae) was measured in the Asiatic rice leafroller, Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae), from twenty locations in China by sequencing wsp, ftsZ and 16S rDNA genes. The results showed high infection rates of Wolbachia in C. medinalis populations. Wolbachia was detected in all geographically separate populations; the average infection rate was ∼ 62.5%, and the highest rates were 90% in Wenzhou and Yangzhou populations. The Wolbachia detected in different C. medinalis populations were 100% identical to each other when wsp, ftsZ, and 16S rDNA sequences were compared, with all sequences belonging to the Wolbachia B supergroup. Based on wsp, ftsZ and 16S rDNA sequences of Wolbachia, three phylogenetic trees of similar pattern emerged. This analysis indicated the possibility of inter-species and intra-species horizontal transmission of Wolbachia in different arthropods in related geographical regions. The migration route of C. medinalis in mainland China was also discussed since large differentiation had been found between the wsp sequences of Chinese and Thai populations

Postdialysis blood pressure rise predicts long-term outcomes in chronic hemodialysis patients: a four-year prospective observational cohort study

<p>Abstract</p> <p>Background</p> <p>The blood pressure (BP) of a proportion of chronic hemodialysis (HD) patients rises after HD. We investigated the influence of postdialysis BP rise on long-term outcomes.</p> <p>Methods</p> <p>A total of 115 prevalent HD patients were enrolled. Because of the fluctuating nature of predialysis and postdialysis BP, systolic BP (SBP) and diastolic BP before and after HD were recorded from 25 consecutive HD sessions during a 2-month period. Patients were followed for 4 years or until death or withdrawal.</p> <p>Results</p> <p>Kaplan-Meier estimates revealed that patients with average postdialysis SBP rise of more than 5 mmHg were at the highest risk of both cardiovascular and all-cause mortality as compared to those with an average postdialysis SBP change between -5 to 5 mmHg and those with an average postdialysis SBP drop of more than 5 mmHg. Furthermore, multivariate Cox regression analysis indicated that both postdialysis SBP rise of more than 5 mmHg (HR, 3.925 [95% CI, 1.410-10.846], <it>p </it>= 0.008) and high cardiothoracic (CT) ratio of more than 50% (HR, 7.560 [95% CI, 2.048-27.912], <it>p </it>= 0.002) independently predicted all-cause mortality. We also found that patients with an average postdialysis SBP rise were associated with subclinical volume overload, as evidenced by the significantly higher CT ratio (<it>p </it>= 0.008).</p> <p>Conclusions</p> <p>A postdialysis SBP rise in HD patients independently predicted 4-year cardiovascular and all-cause mortality. Considering postdialysis SBP rise was associated with higher CT ratio, intensive evaluation of cardiac and volume status should be performed in patients with postdialysis SBP rise.</p