GWFASTA: server for FASTA search in eukaryotic and microbial genomes

Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists

Chirped pulse Raman amplification in plasma: high gain measurements

High power short pulse lasers are usually based on chirped pulse amplification (CPA), where a frequency chirped and temporarily stretched ``seed'' pulse is amplified by a broad-bandwidth solid state medium, which is usually pumped by a monochromatic ``pump'' laser. Here, we demonstrate the feasibility of using chirped pulse Raman amplification (CPRA) as a means of amplifying short pulses in plasma. In this scheme, a short seed pulse is amplified by a stretched and chirped pump pulse through Raman backscattering in a plasma channel. Unlike conventional CPA, each spectral component of the seed is amplified at different longitudinal positions determined by the resonance of the seed, pump and plasma wave, which excites a density echelon that acts as a "chirped'" mirror and simultaneously backscatters and compresses the pump. Experimental evidence shows that it has potential as an ultra-broad bandwidth linear amplifier which dispenses with the need for large compressor gratings

Plasma density measurements using chirped pulse broad-band Raman amplification

Stimulated Raman backscattering is used as a non-destructive method to determine the density of plasma media at localized positions in space and time. By colliding two counter-propagating, ultra-short laser pulses with a spectral bandwidth larger than twice the plasma frequency, amplification occurs at the Stokes wavelengths, which results in regions of gain and loss separated by twice the plasma frequency, from which the plasma density can be deduced. By varying the relative delay between the laser pulses, and therefore the position and timing of the interaction, the spatio-temporal distribution of the plasma density can be mapped out

Chirped pulse Raman amplification in plasma

Raman amplification in plasma has been proposed to be a promising method of amplifying short radiation pulses. Here, we investigate chirped pulse Raman amplification (CPRA) where the pump pulse is chirped and leads to spatiotemporal distributed gain, which exhibits superradiant scaling in the linear regime, usually associated with the nonlinear pump depletion and Compton amplification regimes. CPRA has the potential to serve as a high-efficiency high-fidelity amplifier/compressor stage

Pepper-pot emittance measurement of laser-plasma wakefield accelerated electrons

The transverse emittance is an important parameter governing the brightness of an electron beam. Here we present the first pepper-pot measurement of the transverse emittance for a mono-energetic electron beam from a laser-plasma wakefield accelerator, carried out on the Advanced Laser-Plasma High Energy Accelerators towards X-Rays (ALPHA-X) beam line. Mono-energetic electrons are passed through an array of 52 mu m diameter holes in a tungsten mask. The pepper-pot results set an upper limit for the normalised emittance at 5.5 +/- 1 pi mm mrad for an 82 MeV beam

Near-threshold electron injection in the laser-plasma wakefield accelerator leading to femtosecond bunches

We gratefully acknowledge the support of the UK EPSRC (grant no. EP/J018171/1), the EU FP7 programmes: the Extreme Light Infrastructure (ELI) project, the Laserlab-Europe (no. 284464), and the EUCARD-2 project (no. 312453).The laser-plasma wakefield accelerator is a compact source of high brightness, ultra-short duration electron bunches. Self-injection occurs when electrons from the background plasma gain sufficient momentum at the back of the bubble-shaped accelerating structure to experience sustained acceleration. The shortest duration and highest brightness electron bunches result from self-injection close to the threshold for injection. Here we show that in this case injection is due to the localized charge density build-up in the sheath crossing region at the rear of the bubble, which has the effect of increasing the accelerating potential to above a critical value. Bunch duration is determined by the dwell time above this critical value, which explains why single or multiple ultra-short electron bunches with little dark current are formed in the first bubble. We confirm experimentally, using coherent optical transition radiation measurements, that single or multiple bunches with femtosecond duration and peak currents of several kiloAmpere, and femtosecond intervals between bunches, emerge from the accelerator.Publisher PDFPeer reviewe

Suitability of Killai backwaters for prawn farming-a preliminary micro level survey

Brackishwater areas have been given much importance for prawn farming. No information was available on the Killai backwaters about factors like water quality, topography, contour, extent of the area, tidal amplitude, seed potential and possibilities of flooding etc. Hence during 1982-'84 Klllai area was thoroughly surveyed on the above aspects and the results have been discussed in this paper. From this it is inferred that a total area of about 155 ha is readily available for undertaking both pond and pen culture in this backwater

MULTIPLE QUANTUM WALKERS ON THE LINE USING HYBRID COINS: A POSSIBLE TOOL FOR QUANTUM SEARCH

In this paper discrete quantum walks with different coins used for odd and even time steps are studied. These coins are called hybrid. The calculation results are compared with the most frequently used coin, the Hadamard transform. Furthermore, quantum walks on the line which involve two or more quantum walkers with hybrid coins are studied. Quantum walks with entangled walkers and hybrid coins are also studied. The results of these calculations show that the proposed types of quantum walks can be used for quantum search, because the walker can be directed towards preferred directions and can also be confined in certain segments of the line

Rural-urban disparities in the diagnosis and treatment of hypertension and diabetes among aging Indians

INTRODUCTION: Hypertension and diabetes are modifiable risk factors for dementia. We aimed to assess rural-urban disparities in the diagnosis and treatment of these conditions among aging Indians.METHODS: Participants (n = 6316) were from two parallel, prospective aging cohorts in rural and urban India. Using self-report and clinical/biochemical assessments, we subdivided participants with diabetes and hypertension into undiagnosed and untreated groups. Logistic regression and Fairlie decomposition analysis were the statistical methods utilized.RESULTS: There was a significant rural-urban disparity in undiagnosed hypertension (25.14%), untreated hypertension (11.75%), undiagnosed diabetes (16.94%), and untreated diabetes (11.62%). Further, sociodemographic and lifestyle factors, such as age and tobacco use were the common contributors to the disparities in both undiagnosed hypertension and undiagnosed diabetes, whereas education and body mass index (BMI) were significant contributors to the disparity in untreated hypertension.DISCUSSION: Rural Indians face significant healthcare disadvantages as compared to their urban counterparts, which prompts the urgent need for strategies for equitable healthcare.</p