SciCombinator

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Concept: BLAST

174

BACKGROUND: Mild traumatic brain injury (mTBI) secondary to blast exposure is the most common battlefield injury in Southwest Asia. There has been little prospective work in the combat setting to test the efficacy of new countermeasures. The goal of this study was to compare the efficacy of N-acetyl cysteine (NAC) versus placebo on the symptoms associated with blast exposure mTBI in a combat setting. METHODS: This study was a randomized double blind, placebo-controlled study that was conducted on active duty service members at a forward deployed field hospital in Iraq. All symptomatic U.S. service members who were exposed to significant ordnance blast and who met the criteria for mTBI were offered participation in the study and 81 individuals agreed to participate. Individuals underwent a baseline evaluation and then were randomly assigned to receive either N-acetyl cysteine (NAC) or placebo for seven days. Each subject was re-evaluated at 3 and 7 days. Outcome measures were the presence of the following sequelae of mTBI: dizziness, hearing loss, headache, memory loss, sleep disturbances, and neurocognitive dysfunction. The resolution of these symptoms seven days after the blast exposure was the main outcome measure in this study. Logistic regression on the outcome of ‘no day 7 symptoms’ indicated that NAC treatment was significantly better than placebo (OR = 3.6, p = 0.006). Secondary analysis revealed subjects receiving NAC within 24 hours of blast had an 86% chance of symptom resolution with no reported side effects versus 42% for those seen early who received placebo. CONCLUSION: This study, conducted in an active theatre of war, demonstrates that NAC, a safe pharmaceutical countermeasure, has beneficial effects on the severity and resolution of sequelae of blast induced mTBI. This is the first demonstration of an effective short term countermeasure for mTBI. Further work on long term outcomes and the potential use of NAC in civilian mTBI is warranted. TRIAL REGISTRATION: ClinicalTrials.gov NCT00822263.

Concepts: Brain, Medical terms, Traumatic brain injury, Effectiveness, Term, Post-concussion syndrome, Concussion, BLAST

132

The submarine H.L. Hunley was the first submarine to sink an enemy ship during combat; however, the cause of its sinking has been a mystery for over 150 years. The Hunley set off a 61.2 kg (135 lb) black powder torpedo at a distance less than 5 m (16 ft) off its bow. Scaled experiments were performed that measured black powder and shock tube explosions underwater and propagation of blasts through a model ship hull. This propagation data was used in combination with archival experimental data to evaluate the risk to the crew from their own torpedo. The blast produced likely caused flexion of the ship hull to transmit the blast wave; the secondary wave transmitted inside the crew compartment was of sufficient magnitude that the calculated chances of survival were less than 16% for each crew member. The submarine drifted to its resting place after the crew died of air blast trauma within the hull.

Concepts: Causality, Shock wave, American films, Submarine, Ship, BLAST, Torpedo, Bow

16

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Concepts: DNA, Bioinformatics, Computational phylogenetics, Internet, Sequence alignment, BLAST, Clustal, Web service

7

Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the number and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such analysis usually makes this a time-consuming and very difficult task for users, especially when the primers have a large number of hits. Furthermore, although the BLAST program has been widely used for primer target detection, it is in fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necessarily return complete match information over the entire primer range.

Concepts: DNA, Polymerase chain reaction, DNA replication, DNA polymerase, Primer, BLAST

6

Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST-the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

Concepts: DNA, Bioinformatics, Computational phylogenetics, Computer program, Kinematics, Source code, Sequence alignment, BLAST

4

Throughout the course of a forensic investigation following an explosive attack, the identification and recovery of tissue fragments is of extreme importance. There are few universally accepted methods to achieve this end. This project aims to explore this issue through the examination of the spatial distribution of the tissue fragments resulting from an explosive event. To address this, a two stage pilot study was conducted: first, a series of controlled explosions on porcine carcases was undertaken. Second, the data produced from these explosions were used to chart the spatial distribution of the tissue debris. In the controlled explosions, 3kg military grade explosive was chosen to create the maximum amount of fragmentation; this level of explosive also prevented the complete disappearance of forensic evidence through evaporation. Additionally, the blast created by military grade explosive is highly powerful and would mean that the maximum possible distance was achieved and would therefore allow the recorded distances and pattern spread to be a guideline for forensic recovery of associated with an explosive amount of an unknown size and quality. A total station was employed to record the location of the resulting forensic evidence, with the collected data analysed using R Studio. The observed patterns suggested that the distribution of remains is fairly consistent in trials under similar environmental conditions. This indicates potential for some general guidelines for forensic evidence collection (for example, the distance from the explosion that a search should cover).

Concepts: Fragment, Distance, Spread Toolkit, BLAST, Explosion

3

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. This freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.

Concepts: Bioinformatics, Amino acid, Parallel computing, Computer program, Computer science, Grid computing, Central processing unit, BLAST

2

We propose SW#, a new CUDA GPU enabled and memory efficient implementation of dynamic programming algorithms for local alignment. It can be use as either a standalone application or a library. Although there are other GPU implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

Concepts: Algorithm, Computer, Computer program, Computer programming, Dynamic programming, BLAST, Smith–Waterman algorithm, Levenshtein distance

2

The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.

Concepts: Bioinformatics, Computational phylogenetics, Searching, Sequence alignment, Dynamic programming, BLAST, FASTA, Smith–Waterman algorithm

1

Over the last decades, vast numbers of sequences were deposited in public databases. Bioinformatics tools allow homology and consequently functional inference for these sequences. New profile-based homology search tools have been introduced, allowing reliable detection of remote homologs, but have not been systematically benchmarked. To provide such a comparison, which can guide bioinformatics workflows, we extend and apply our previously developed benchmark approach to evaluate the “next generation” of profile-based approaches, including CS-BLAST, HHSEARCH and PHMMER, in comparison with the non-profile based search tools NCBI-BLAST, USEARCH, UBLAST and FASTA.

Concepts: Bioinformatics, Star Trek: The Next Generation, Next Generation, Benchmarking, BLAST