Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Primary Blast Traumatic Brain Injury in the Rat: Relating Diffusion Tensor Imaging and Behavior

The incidence of traumatic brain injury (TBI) among military personnel is at its highest point in U.S. history. Experimental animal models of blast have provided a wealth of insight into blast injury. The mechanisms of neurotrauma caused by blast, however, are still under debate. Specifically, it is unclear whether the blast shockwave in the absence of head motion is sufficient to induce brain trauma. In this study, the consequences of blast injury were investigated in a rat model of primary blast TBI. Animals were exposed to blast shockwaves with peak reflected overpressures of either 100 or 450 kPa (39 and 110 kPa incident pressure, respectively) and subsequently underwent a battery of behavioral tests. Diffusion tensor imaging (DTI), a promising method to detect blast injury in humans, was performed on fixed brains to detect and visualize the spatial dependence of blast injury. Blast TBI caused significant deficits in memory function as evidenced by the Morris Water Maze, but limited emotional deficits as evidenced by the Open Field Test and Elevated Plus Maze. Fractional anisotropy, a metric derived from DTI, revealed significant brain abnormalities in blast-exposed animals. A significant relationship between memory deficits and brain microstructure was evident in the hippocampus, consistent with its role in memory function. The results provide fundamental insight into the neurological consequences of blast TBI, including the evolution of injury during the sub-acute phase and the spatially dependent pattern of injury. The relationship between memory dysfunction and microstructural brain abnormalities may provide insight into the persistent cognitive difficulties experienced by soldiers exposed to blast neurotrauma and may be important to guide therapeutic and rehabilitative efforts

A Thoracic Mechanism of Mild Traumatic Brain Injury Due to Blast Pressure Waves

The mechanisms by which blast pressure waves cause mild to moderate traumatic brain injury (mTBI) are an open question. Possibilities include acceleration of the head, direct passage of the blast wave via the cranium, and propagation of the blast wave to the brain via a thoracic mechanism. The hypothesis that the blast pressure wave reaches the brain via a thoracic mechanism is considered in light of ballistic and blast pressure wave research. Ballistic pressure waves, caused by penetrating ballistic projectiles or ballistic impacts to body armor, can only reach the brain via an internal mechanism and have been shown to cause cerebral effects. Similar effects have been documented when a blast pressure wave has been applied to the whole body or focused on the thorax in animal models. While vagotomy reduces apnea and bradycardia due to ballistic or blast pressure waves, it does not eliminate neural damage in the brain, suggesting that the pressure wave directly affects the brain cells via a thoracic mechanism. An experiment is proposed which isolates the thoracic mechanism from cranial mechanisms of mTBI due to blast wave exposure. Results have implications for evaluating risk of mTBI due to blast exposure and for developing effective protection

Cropping system to limit blast disease in upland rice

Cropping system is an essential aspect to take into account to manage blast disease (caused by the fungus Magnaporthe oryzae). In addition to the selection of resistant cultivars, studies report opportunities to limit blast incidence by managing mineral amendment (N, Si, P, etc.), cultivar mixtures or other cropping system adaptations. In Madagascar, rice is the staple crop and food. Farmers traditionally grow irrigated or rainfed lowland rice wherever possible. In the mid-1980s, CIRAD and FOFIFA launched a research program for the highlands to extend upland rice growing areas in high elevation areas of the tropics. This program was consolidated with research on cropping practices that ensure the sustainability of upland rice based cropping systems in this poor and fragile environment. New varieties where obtained, adapted for rainfed cropping up to 1800 m altitude (Dzido et al., 2004). However, farmers had to face attacks of blast disease. Due to the small genetic basis of these varieties, the fungus quickly overcame resistant or tolerant lines selected by breeders. The ways of management of blast disease are very limited in a country like Madagascar where efficient solutions are often not suitable for farmers. Observations of blast epidemics in different regions made us consider the soil as a key factor for rice susceptibility. In a first experiment, we measured the potential of our very susceptible varieties to tolerate blast when cropped in different soil conditions. During two years, we transported volcanic soil from a very fertile area close to the experimentation site and where blast pressure is much lower. We observed a decrease of blast symptoms on rice cropped on that soil compared to the soil of the experimental site, both on leaves and panicles. That decrease was bound to a significant yield increase, demonstrating the importance of plant nutrition on blast incidence. Such results confirm those obtained in 1981 by Seguy et al. Our aim was then to develop cropping systems that could influence blast incidence through an improvement of soil functions. Direct seeded mulch based (DSMB) cropping systems were first used in Madagascar to limit erosion in upland areas. During 4 years, we compared blast epidemics between a traditional cropping system with ploughing each year and a DSMB cropping system, on a midsusceptible variety specific of the highlands conditions. Two fertilisation levels were also tested in these systems: zebu manure only and manure plus additional mineral fertiliser. A significant difference between the two systems was observed, both at leaf and panicle stage. Blast incidence was reduced in DSMB cropping system and, on the contrary to the traditional cropping system, the mineral fertilisation had no effect on blast in DSMB. N fertilisation is known for a long time as an essential factor in blast management. The fact that DSMB cropping system reduced the effect of N-fertilisation made us consider N as the determinant factor of the interaction between cropping system and blast incidence. The determinants of this interaction must then be explained to enable new and durable cropping systems to be developed to manage blast epidemics, in addition to cultivar improvement. This is the objectives of the starting project GARP (ANR-Systerra) which is conducted in Bolivia, Brazil, France, and Madagascar. Its aim is to quantify the interactions between cropping system, N-nutrition and blast resistance in upland rice. Hypotheses and preliminary results of the project will be presented. (Texte intégral

Panoramic Views of the Cygnus Loop

We present a complete atlas of the Cygnus Loop supernova remnant in the light of [O III] (5007), H alpha, and [S II] (6717, 6731). Despite its shell-like appearance, the Cygnus Loop is not a current example of a Sedov-Taylor blast wave. Rather, the optical emission traces interactions of the supernova blast wave with clumps of gas. The surrounding interstellar medium forms the walls of a cavity through which the blast wave now propagates, including a nearly complete shell in which non-radiative filaments are detected. The Cygnus Loop blast wave is not breaking out of a dense cloud, but is instead running into confining walls. The interstellar medium dominates not only the appearance of the Cygnus Loop but also the continued evolution of the blast wave. If this is a typical example of a supernova remnant, then global models of the interstellar medium must account for such significant blast wave deceleration.Comment: 28 pages AAS Latex, 28 black+white figures, 6 color figures. To be published in The Astrophysical Journal Supplement Serie

A Semi-analytic Formulation for Relativistic Blast Waves with a Long-lived Reverse Shock

This paper performs a semi-analytic study of relativistic blast waves in the context of gamma-ray bursts (GRBs). Although commonly used in a wide range of analytical and numerical studies, the equation of state (EOS) with a constant adiabatic index is a poor approximation for relativistic hydrodynamics. Adopting a more realistic EOS with a variable adiabatic index, we present a simple form of jump conditions for relativistic hydrodynamical shocks. Then we describe in detail our technique of modeling a very general class of GRB blast waves with a long-lived reverse shock. Our technique admits an arbitrary radial stratification of the ejecta and ambient medium. We use two different methods to find dynamics of the blast wave: (1) customary pressure balance across the blast wave and (2) the "mechanical model". Using a simple example model, we demonstrate that the two methods yield significantly different dynamical evolutions of the blast wave. We show that the pressure balance does not satisfy the energy conservation for an adiabatic blast wave while the mechanical model does. We also compare two sets of afterglow light curves obtained with the two different methods.Comment: 33 pages, 9 figures, published in Ap